Jun 25, 2026
Version 2
P. falciparum microhaplotype deep sequencing assays V.2
- Anjana Rai1,
- Ashley Osborne1,
- Kian Soon Hoon1,
- Hidayat Trimarsanto1,
- Kim Piera1,
- Angela Rumaseb1,
- Edwin Sutanto1,
- Sarah Auburn1
- 1Menzies School of Health Research and Charles Darwin University
- Malaria_NGS
Protocol Citation: Anjana Rai, Ashley Osborne, Kian Soon Hoon, Hidayat Trimarsanto, Kim Piera, Angela Rumaseb, Edwin Sutanto, Sarah Auburn 2026. P. falciparum microhaplotype deep sequencing assays. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ld4od9l5b/v2Version created by Anjana Rai
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: June 25, 2026
Last Modified: June 25, 2026
Protocol Integer ID: 319803
Keywords: Plasmodium falciparum, microhaplotype, rhAmpSeq, amplicon sequencing, Illumina, Plasmodium falciparum marker, deep sequencing assay, plasmodium species marker, microhaplotype loci high diversity snp, drug resistance marker, diagnostic marker, infection diveristy, charecterization of infection diversity, integrated DNA technologies, multiplexed PCR, plasmodium species confirmation marker, established plasmodium vivax, plasmodium vivax, deep sequencing assay, microhaplotype, drug resistance marker, diversity snp, diagnostic marker, falciparum panel, throughput rhampseq library preparation protocol
Funders Acknowledgements:
NHMRC Investigator grant awarded to Auburn
Grant ID: GNT2025377
Menzies Small Grant awarded to Rai
Grant ID: 2025 Menzies Small Grant
Abstract
This SOP is adapted from a previously established Plasmodium vivax high-throughput rhAmpSeq library preparation protocol developed by Integrated DNA Technologies (IDT)1. Building on this framework, a selection of markers from the two most widely used P. falciparum (Pf) genotyping panels, SpotMalaria2 (widely used in the Asia-Pacific; 137 markers) and MAD4HatTeR3 (widely used in Africa; 276 markers), were combined into a single P. falciparum panel comprising 237 markers across two multiplexes (A and B). The SOP describes the laboratory procedures for high-throughput amplification of the two multiplexes of 120 (A) and 117 (B) P. falciparum markers for downstream genotyping by sequencing on the Illumina platform. The 237 markers include a panel of 203 microhaplotype (loci comprising 3 or more globally high-diversity SNPs) distributed across the P. falciparum genome, 19 drug resistance markers, 10 diagnostic markers, and five Plasmodium species confirmation markers. Diagnostic markers are still in development, and caution should be taken when using them. It is advised to include positive, human and non-template controls in each run.
We welcome any questions and/or feedback on the protocol.
Materials
| A | B | C | D | |
| Reagents | Supplier | Size | Catalog # | |
| IDTE, pH 7.5 | IDT | 10 x 2 mL | 11-01-02-02 | |
| IDTE pH 8.0 | IDT | 10 x 2 mL | 11-01-02-05 | |
| Nuclease-Free Water | IDT | 10 x 2 mL | 11-04-02-01 | |
| rhAmpSeq Library Kit | IDT | 16 rxn 100 rxn 500 rxn 5000 rxn | 10000064 10000065 10000066 10000067 | |
| rhAmpSeq pf custom PCR panel | IDT | 8nmol | Sales Order #9520068 | |
| xGen 10nt UDI Index Primer Plates | IDT | Plate 1-4 Plate 1-8 Plate 1-16 | 10008052 10008053 10008054 | |
| SPRIselect | Beckman Coulter | 5 mL 60 mL 450 mL | B23317 B23318 B23319 | |
| Ethanol (200 proof) | ||||
| High Sensivity D1000 ScreenTape | Agilent | 7 ScreenTapes | AG 5067-5584 | |
| High Sensitivity D1000 Reagents (Include ladder & sample buffer) | Agilent | 112 reactions | AG 5067-5585 | |
| Collibri Library Quantification Kit | Invitrogen | A38524500 | ||
| Agarose | ||||
| SybrSafe | Invitrogen | S33102 | ||
| Consumables | ||||
| DNA LoBind Tubes and 96-well/V plate | Eppendorf | 250 pcs (1.5 mL) 250 pcs (2 mL) 5 bags (16 plates) | 022431021 022431048 0030603303 | |
| Eppendorf twin.tec microbiology PCR Plate 96, semi-skirted, 250 µL | Eppendorf | 10 pcs | 0030129326 | |
| Axygen 8-Strip PCR Tubes, 0.2 mL | Thermo Fisher Scientific | 125 pcs | 14-222-251 | |
| Qubit assay tubes | Thermo Fisher Scientific | 500 pcs | Q32856 | |
| Microseal 'B' PCR Plate Sealing Film | Bio-Rad | 100 pcs | MSB1001 | |
| Agilent Loading Tips | Agilent | 112 pcs | AG 5067-5598 | |
| Agilent Strip caps | Agilent | 120 pcs | AG 401425 | |
| Agilent Optical tube strip | Agilent | 120 pcs | AG 401428 | |
| Equipment | ||||
| DynaMag-2 Magnet or equivalent | Thermo Fisher Scientific | 12321D | ||
| Agilent 4150 TapeStation or agarose gel imaging system (e.g. GelDoc) | Agilent/Bio-Rad | |||
| 96-well thermocycler | ||||
| Microcentrifuge | ||||
| Vortex | ||||
| Centrifuge with plate adapter |
List of PfrhAmpSeq primers
| Target ID | Primer Sequence 5' - 3' | Pool name | |
| RH.0497C4ABA81D4DCZ0Z.F | /rhSeq-f/CCATTGTTAGGATATTCTTTTGTTTCTTrCTTTC/GT1/ | Primary | |
| RH.D4CF7FFBA317440Z0Z.F | /rhSeq-f/GAAATTTTTGCATTATCGTCTAAGGATTrGTTGG/GT1/ | Primary | |
| RH.185FC2677E87465Z0Z.F | /rhSeq-f/AGCCAAAATAACTGCATGTGArGTTGC/GT1/ | Primary | |
| RH.98FBF17848474D4Z0Z.F | /rhSeq-f/GTACACACAAATATAAATGTACCACAAArCACAT/GT2/ | Primary | |
| RH.9139B312704A4E9Z0Z.F | /rhSeq-f/CTGACGAACCACATATATTTACACAATrGGAAT/GT4/ | Primary | |
| RH.B38DB0661D5B44AZ0Z.F | /rhSeq-f/GCTTTTTCAAACCTTTCATTATTGTTTTrCATTC/GT1/ | Primary | |
| RH.6D01A460621D4B8Z0Z.F | /rhSeq-f/GTACCACTATTAAACCAATCAACAAAArGCTGA/GT1/ | Primary | |
| RH.99B19FA8FE354E1Z0Z.F | /rhSeq-f/CAACCAAGAAAAATAGCTGTAAAAAGTrATTTG/GT1/ | Primary | |
| RH.F138A426CEC84A7Z0Z.F | /rhSeq-f/GCTATCATTACATGCTGACACAATATrCATGA/GT1/ | Primary | |
| RH.DDCC9C2ED006492Z0Z.F | /rhSeq-f/TCAAAGTGCTACTTGGTACTTCTrCCTTT/GT3/ | Primary | |
| RH.2030081C2E8943FZ0Z.F | /rhSeq-f/TCAACACAAACAGCCTTCATAAArGGGTC/GT3/ | Primary | |
| RH.4CD8D0A7AB434AAZ0Z.F | /rhSeq-f/TGAAGAATATTGACATGAAACATTATAATrACACA/GT1/ | Primary | |
| RH.DF8645D2839649BZ0Z.F | /rhSeq-f/GCATTAAGAAAACATGGCTCTTTACTTArCAGTC/GT4/ | Primary | |
| RH.20D4370B5668462Z0Z.F | /rhSeq-f/TCATCTGAGGTAGATGATGAATTAAArGGTTT/GT1/ | Primary | |
| RH.2A4E2CF43E434E5Z0Z.F | /rhSeq-f/TCAAATGTATATTGTTCTCCTCATAAGArACTAT/GT4/ | Primary | |
| RH.56288DD4BDA2437Z0Z.F | /rhSeq-f/TCTGGAATAGGAACAAAGTGATTATGrGCAAA/GT4/ | Primary | |
| RH.E0A3D130866C4EBZ0Z.F | /rhSeq-f/AAGTTTATTCTGGAGTCAAATAGGAArCGAGT/GT2/ | Primary | |
| RH.5F8779D16F6B4D1Z0Z.F | /rhSeq-f/GATAGAGAAAATGAATCTATGCCTCATrAAAAT/GT4/ | Primary | |
| RH.052C82782DD94B4Z0Z.F | /rhSeq-f/TTTGGACACCGTGTAATAGATTTTrAATGA/GT4/ | Primary | |
| RH.66FC5A65D6224F4Z0Z.F | /rhSeq-f/CTATTCTGTTTCTTTTGTTCCATGTTrATAAA/GT4/ | Primary | |
| RH.05877E4991BC46EZ0Z.F | /rhSeq-f/ATCATCCTTTTTACCATTTAAATTTATGTrCCACA/GT1/ | Primary | |
| RH.0D67565F4C3847CZ0Z.F | /rhSeq-f/CATCTTAACAAAAGCTCTATGAACTTCTrGTATC/GT1/ | Primary | |
| RH.1C412A6096B24B6Z0Z.F | /rhSeq-f/TCGACTAGACATGAAAAATTCAGATTrGAGGT/GT4/ | Primary | |
| RH.DADD4A1EC493407Z0Z.F | /rhSeq-f/ACTACACATTTAGAGGTCTAGGAAATAAArGGAGT/GT4/ | Primary | |
| RH.131BA01846444AFZ0Z.F | /rhSeq-f/GAGAATCTATTCCACCTACCAATATrAAAAC/GT4/ | Primary | |
| RH.2A936B6612214C0Z0Z.F | /rhSeq-f/CAAGCTACTACCCAAAATGATAAATCTTrCTTCA/GT1/ | Primary | |
| RH.77FE64C8830A46AZ0Z.F | /rhSeq-f/TGGATTAAACGCTGATATGTCTGATrGACGG/GT1/ | Primary | |
| RH.63B2C6ECC87D409Z0Z.F | /rhSeq-f/GAACCAAACAACGACAAAGGAArCAAGA/GT1/ | Primary | |
| RH.73E1E039A8E1486Z0Z.F | /rhSeq-f/AGAAGCATCTTCACTCGTACATArCACAA/GT1/ | Primary | |
| RH.9A45E2C5DDFB41FZ0Z.F | /rhSeq-f/CGTTAATGCAATCATTCCACATGTArCGTAA/GT4/ | Primary | |
| RH.741CE999A6054F5Z0Z.F | /rhSeq-f/ATCAGGGCAATTTTATTAGATTTGAAAArGAAGA/GT4/ | Primary | |
| RH.AC0C4ED33EB8436Z0Z.F | /rhSeq-f/GGGTTCCTCACAAATGTTATTTTCTrATATG/GT4/ | Primary | |
| RH.D9EE34B6F40F4D4Z0Z.F | /rhSeq-f/AGTATACATATCTAACAACACACTTTTrATTCC/GT1/ | Primary | |
| RH.A35B05759EF241AZ0Z.F | /rhSeq-f/GTGGAGAGGTAACACATACTGATGrCAAAT/GT4/ | Primary | |
| RH.00861D1F91E04CEZ0Z.F | /rhSeq-f/GTTGGTTAGAATGGAGTGATCTTTTArGAGAA/GT2/ | Primary | |
| RH.7AFA5825BCFF48CZ0Z.F | /rhSeq-f/ATCTTTGAGATATGATTCGGCCATTTrCGATA/GT4/ | Primary | |
| RH.3FFB4791AAB740BZ0Z.F | /rhSeq-f/GTCTCATTACCAAATTCAAATACTTCTTrCACTT/GT4/ | Primary | |
| RH.0909F225F86B448Z0Z.F | /rhSeq-f/CGAATATACACCCAGAAATATAAATGGAArCACAA/GT4/ | Primary | |
| RH.E89C0AE29BF4491Z0Z.F | /rhSeq-f/GGATACATTACAACGTTCAATAAGCTrAAATG/GT1/ | Primary | |
| RH.DEFD198774AA4F7Z0Z.F | /rhSeq-f/GAATCAAAACTTATTGCTACCGTAATArCCTAA/GT4/ | Primary | |
| RH.1237EDEE873F4BFZ0Z.F | /rhSeq-f/TTCTTTAGAATTTAAAACGAAGTCTTCATrATTCT/GT1/ | Primary | |
| RH.013BA341493646EZ0Z.F | /rhSeq-f/GGGTAGATATCGTTATAAGGGCTrATAAT/GT2/ | Primary | |
| RH.125DEC55F816487Z0Z.F | /rhSeq-f/AATGAATTTTCAAACCAATCTGGATrCTGCA/GT2/ | Primary | |
| RH.75608D9B4B37452Z0Z.F | /rhSeq-f/GGCTTTTGGATTTAGTAGTTCTAGAATArGCATG/GT4/ | Primary | |
| RH.234D1D1718AE438Z0Z.F | /rhSeq-f/GTCCTTTTGCATTTTTGCTAAACAArGTTAT/GT1/ | Primary | |
| RH.A2EEDF3F7C3C489Z0Z.F | /rhSeq-f/CAATTTTTACATATGCCAGTTCCTTTTTArGGTTT/GT3/ | Primary | |
| RH.084717DAABF3455Z0Z.F | /rhSeq-f/CATTTTTGTTATCCTGAGTTTTAAGTrGAATG/GT4/ | Primary | |
| RH.FC2A8FBE072E409Z0Z.F | /rhSeq-f/CATTAATTTTATGATGAAGGTGTGGGrGAGCT/GT1/ | Primary | |
| RH.474DC1ABE955486Z0Z.F | /rhSeq-f/CATATTCAAATGACCCTGAGCTAArCATCT/GT1/ | Primary | |
| RH.0D3AB1C35D2C45EZ0Z.F | /rhSeq-f/AAGTCCAAGTGAACAACGACrCTGCT/GT1/ | Primary | |
| RH.34536B047B76468Z0Z.F | /rhSeq-f/GCCATTGATTTAACTCTCCATGAATrGTTCA/GT2/ | Primary | |
| RH.3D49C933215B47CZ0Z.F | /rhSeq-f/CAAAATTGCCTATCATTAATGGAAAATATrCCTCA/GT1/ | Primary | |
| RH.8FBEEDC5DA7144EZ0Z.F | /rhSeq-f/CCAATTCCATGTATATTCATCATTAATTTrCGTTA/GT4/ | Primary | |
| RH.BBAD704FF905480Z0Z.F | /rhSeq-f/CTTTTGGTACAACAATTGTTCAAGGrGAAGA/GT4/ | Primary | |
| RH.31A583D2771B455Z0Z.F | /rhSeq-f/GGCATACGTTATCGAAAGAATATGAAArCTCAA/GT4/ | Primary | |
| RH.D222DAB4B6474B5Z0Z.F | /rhSeq-f/TCTCCATTTTGATCATTTAACAACTTrATCAT/GT3/ | Primary | |
| RH.391355D65D9E4C4Z0Z.F | /rhSeq-f/TACAACAGGAGGAAATACAAAATATAATrACTTT/GT3/ | Primary | |
| RH.B50875B83BA8432Z0Z.F | /rhSeq-f/GTGATGAATACCATATAGCCCTTTrCAAAT/GT1/ | Primary | |
| RH.F28E178506994BFZ0Z.F | /rhSeq-f/GGGATGATTATTATTGTTATTATGAGTTTrGGTTC/GT2/ | Primary | |
| RH.3A58F1684211457Z0Z.F | /rhSeq-f/GTACCTGGTGATAATATGTCTAGAGArCGAAT/GT1/ | Primary | |
| RH.627F76C560224A6Z0Z.F | /rhSeq-f/GAAATGTAAGCTCAAGCGCTAGTATAArGTGAA/GT4/ | Primary | |
| RH.72697B5F4E304E6Z0Z.F | /rhSeq-f/GATACACCATTGTCTTGGATATTATTTTrGATCG/GT1/ | Primary | |
| RH.B7D7C030BE2C432Z0Z.F | /rhSeq-f/GATTATGGACATCTTGCTATGGGrAAATG/GT4/ | Primary | |
| RH.68BE559FDD564A3Z0Z.F | /rhSeq-f/GATAATGATCCTGCAGTAGTAAGTrGGTAG/GT4/ | Primary | |
| RH.5193318E754A417Z0Z.F | /rhSeq-f/GAATTTAATCTCTCACCATTAGTTCCArCCAAT/GT2/ | Primary | |
| RH.46659BEDBC00438Z0Z.F | /rhSeq-f/GACTTGGGTATCTTTTCCATATATAATAArCGCAT/GT2/ | Primary | |
| RH.153CD64285C0471Z0Z.F | /rhSeq-f/GTTACTTTAGAAACACAATCCATGATAGrCACAC/GT2/ | Primary | |
| RH.98F4419B5559408Z0Z.F | /rhSeq-f/CATCTCTTGTTGTTACTTGTCCTrCCACA/GT4/ | Primary | |
| RH.654F6CF05F274F6Z0Z.F | /rhSeq-f/GAAGTTTTCAAAATTGATGACATTGATAArCCGTT/GT1/ | Primary | |
| RH.64BEC91228CA4FEZ0Z.F | /rhSeq-f/CATGAATGATGACTACTCCAATCAAAATArATATG/GT4/ | Primary | |
| RH.904F67856AF2484Z0Z.F | /rhSeq-f/CCGATCATCAAGCCGAATATATACCrAATAA/GT1/ | Primary | |
| RH.0BF6BBF4558B415Z0Z.F | /rhSeq-f/GATTTGCCTACAATATTTGCACATTTrGATTC/GT1/ | Primary | |
| RH.B8439DE2510B4D4Z0Z.F | /rhSeq-f/AGTGAATGTATGAGTATGTTAATAGATGArGTGGA/GT4/ | Primary | |
| RH.3792106A3B37488Z0Z.F | /rhSeq-f/AAAGCAGTACCATCTATATCTCTTrCCTTT/GT1/ | Primary | |
| RH.90ABC72D97AC491Z0Z.F | /rhSeq-f/TCATGAATATGTTTTCCTGATACATAAATrAGTCT/GT1/ | Primary | |
| RH.C3822EB7E8094CDZ0Z.F | /rhSeq-f/CTAAGGAAAAGGAAATTCGCTCrGGGAC/GT4/ | Primary | |
| RH.DE684B76F521431Z0Z.F | /rhSeq-f/GTTCTTGTCTTGGTAAATGTGCTrCATGT/GT2/ | Primary | |
| RH.DC31D3E7CDF041EZ0Z.F | /rhSeq-f/ACATTATGGGTTACGTTAAGTAGTACrCTTTG/GT2/ | Primary | |
| RH.CB5AE1573D5D439Z0Z.F | /rhSeq-f/GAACATATGAAATTCAAGAGGAAATAAAArAAGAA/GT4/ | Primary | |
| RH.C8EC2CED2C9B4DAZ0Z.F | /rhSeq-f/ATTGACCCTATGCTAAAACTGAArCGAAA/GT2/ | Primary | |
| RH.C1E1BF8D6809480Z0Z.F | /rhSeq-f/TCTGACAATATGGCTAGTAACAGTArCAGCT/GT4/ | Primary | |
| RH.4188BDD618CA401Z0Z.F | /rhSeq-f/CTATTCGTATAGGTTTCACTAAGTTATCTrAAAAT/GT1/ | Primary | |
| RH.A33E8496E4FC488Z0Z.F | /rhSeq-f/CCAAAAACATGGAAACCTACCATTTTTrCTTTT/GT3/ | Primary | |
| RH.ADA7632A77F2409Z0Z.F | /rhSeq-f/AAAATAATCATGACAAAGAAACATGTrGGTCA/GT3/ | Primary | |
| RH.F2DA4EADF4644AAZ0Z.F | /rhSeq-f/GAAAATTTCGAGCAACTTTTCTTTTTArGATTT/GT3/ | Primary | |
| RH.A79623D3D0BA4D4Z0Z.F | /rhSeq-f/GTTCTTTATTACAAGAGCTAAGAAAACATrATAGA/GT4/ | Primary | |
| RH.130807648D6D4A0Z0Z.F | /rhSeq-f/GACAAATATAAGAAACATCCCAGGAACrCATAC/GT1/ | Primary | |
| RH.0A4FC70E2BA842CZ0Z.F | /rhSeq-f/CGTTTTCATGAAAGGAGTATCCAATrAAATG/GT4/ | Primary | |
| RH.C49AA0D57A3A410Z0Z.F | /rhSeq-f/CCAACATTTTCTTATTCGATCTGTArCCTTC/GT4/ | Primary | |
| RH.F6918FA0DE0E46BZ0Z.F | /rhSeq-f/ATGATCAAAATATGGATAATATGAATCAArAAAGG/GT2/ | Primary | |
| RH.E9048996E241498Z0Z.F | /rhSeq-f/CATTTATGGAATCATACACTTGGTGTrAAATA/GT4/ | Primary | |
| RH.54525BCEFAE640DZ0Z.F | /rhSeq-f/CTTTAAATAAAACTAACACATCTAATGCArCCATC/GT4/ | Primary | |
| RH.50101BFA0F6142AZ0Z.F | /rhSeq-f/GAAAATATGTCAAGCGGAGTTTTTrGCATT/GT1/ | Primary | |
| RH.90A6B553AA964B7Z0Z.F | /rhSeq-f/TGAGGCTTCATGTAAGATATCAATTGrCTTCC/GT4/ | Primary | |
| RH.CA42B27342E04EEZ0Z.F | /rhSeq-f/CGTAGCACCTAAACAGGAArGTGAA/GT1/ | Primary | |
| RH.59246A4CA5304FEZ0Z.F | /rhSeq-f/TGGTCCTTCTATTACCATTAAAGGTTrCATTA/GT2/ | Primary | |
| RH.6302E667853A4ECZ0Z.F | /rhSeq-f/CTATATGTTCGAGCATGGATAATTTACrCCGAT/GT1/ | Primary | |
| RH.1E3DF893CA764FEZ0Z.F | /rhSeq-f/AGATTGGTTTTGTGATTTAAAAGAAArCGTTG/GT4/ | Primary | |
| RH.48A63D3D7846478Z0Z.F | /rhSeq-f/CATGTTTCAATATTCAGACGCATTTrGATTC/GT1/ | Primary | |
| RH.8D667234A62A4DFZ0Z.F | /rhSeq-f/CAAATAATCTTGTACCATCAACACTATATrGCAAA/GT3/ | Primary | |
| RH.1E5857F6734342DZ0Z.F | /rhSeq-f/GAAAACATATCACTAGATCCATTACCrCACGG/GT2/ | Primary | |
| RH.9DBEDAA38D9D4A7Z0Z.F | /rhSeq-f/GTCATAAGGGAACCTAAATTATTAGTATrAATCG/GT1/ | Primary | |
| RH.AE16A161DEEF472Z0Z.F | /rhSeq-f/GGTAGTTCAGTTGGATAGAATGCrCCGAC/GT1/ | Primary | |
| RH.0E85C0E0F5434A6Z0Z.F | /rhSeq-f/ATATTTCAAATATCCAACCGCTTCArGGAAC/GT1/ | Primary | |
| RH.414A94632E804D2Z0Z.F | /rhSeq-f/CAAAGTTGAAGATCTAATAGTTTTACTTrGGGAA/GT4/ | Primary | |
| RH.285DF9E0E6EC45AZ0Z.F | /rhSeq-f/TCCTATATGGGTAATTAGTAGTTCCArATCAT/GT1/ | Primary | |
| RH.D9BA7A7DDA2443CZ0Z.F | /rhSeq-f/TTTATTTCCTGTTCATCTGAGGTTTTrCTTTT/GT2/ | Primary | |
| RH.73818732C84143EZ0Z.F | /rhSeq-f/TGCTTTCAGATTTGAAACTAATGATTTrGATTG/GT1/ | Primary | |
| RH.1CA07193BAC44D7Z0Z.F | /rhSeq-f/GACCACATTGAAATCCGACAATTTrCATTT/GT2/ | Primary | |
| RH.4178D0F094A242CZ0Z.F | /rhSeq-f/CCTTCATAACATATAGCAGCATATGTrGTTAC/GT4/ | Primary | |
| RH.243246A73EA94F4Z0Z.F | /rhSeq-f/CTAAATTCTGTCCCTTCACCTAAArGTTTC/GT4/ | Primary | |
| RH.264EFB3D472D490Z0Z.F | /rhSeq-f/CCTGTTCAGATAACTTTGGGAATrCGATT/GT1/ | Primary | |
| RH.F462CC064314480Z0Z.F | /rhSeq-f/TGTGAATAGTATTACCTTAAATGTGGGrCGCAA/GT4/ | Primary | |
| RH.0F8E7CF2B5A44F8Z0Z.F | /rhSeq-f/CATATACTATTGTTAGTTGTATACAAGGTrCCAGC/GT4/ | Primary | |
| RH.45D97578522E475Z0Z.F | /rhSeq-f/AGCAGCTGTACCTCTAATAATTTTCATrAATAA/GT4/ | Primary | |
| RH.A697335E3F5046EZ0Z.F | /rhSeq-f/TAGATTCAGTAGATGGACCTTCArGAACC/GT1/ | Primary | |
| RH.F2DC0BDE0240494Z0Z.F | /rhSeq-f/GGCTCCAAGAGTGTTAATAATACTArCAGCT/GT4/ | Primary | |
| RH.DA3C260CCDD546EZ0Z.F | /rhSeq-f/GTTTAGCTTTTTCACATTGTGTTCTTAATrCTTCT/GT1/ | Primary | |
| RH.345B0264CAD84F1Z0Z.F | /rhSeq-f/GGCAGAATAGAAAACGGACAAAArGAATG/GT2/ | Primary | |
| RH.0497C4ABA81D4DCZ0Z.R | /rhSeq-r/GATAATTTGAATGAACCACATTTTAAACArAACTC/GT4/ | Primary | |
| RH.D4CF7FFBA317440Z0Z.R | /rhSeq-r/GCAATGTTCATTGAACTCTTTGATATCTrCAGAA/GT4/ | Primary | |
| RH.185FC2677E87465Z0Z.R | /rhSeq-r/GTGGCATTCGTTGGATCArCATGG/GT2/ | Primary | |
| RH.98FBF17848474D4Z0Z.R | /rhSeq-r/GAGTGATTAGTATTTCGAGATAATTCTTrCAGCT/GT4/ | Primary | |
| RH.9139B312704A4E9Z0Z.R | /rhSeq-r/GATTTGGAATATACTACTTGTGCCAATrCAAAA/GT4/ | Primary | |
| RH.B38DB0661D5B44AZ0Z.R | /rhSeq-r/AGCCAAAATAGTTTAAATCTATACTTGTrCTCAC/GT3/ | Primary | |
| RH.6D01A460621D4B8Z0Z.R | /rhSeq-r/CCAAGGAAGGTAGAATATCAAATACAArGGGAT/GT2/ | Primary | |
| RH.99B19FA8FE354E1Z0Z.R | /rhSeq-r/CCATATTTATACTTCTTTCATGTGCTTrCATCA/GT4/ | Primary | |
| RH.F138A426CEC84A7Z0Z.R | /rhSeq-r/GTTGTGGAGATGATAAAACTATCAAATTrCTGGT/GT2/ | Primary | |
| RH.DDCC9C2ED006492Z0Z.R | /rhSeq-r/AAAGCAACAGGTACAAGATTTTCTrAGATC/GT1/ | Primary | |
| RH.2030081C2E8943FZ0Z.R | /rhSeq-r/TCAATTAGTTGTTATATTAACAGATGGArATTCC/GT4/ | Primary | |
| RH.4CD8D0A7AB434AAZ0Z.R | /rhSeq-r/GTATGTATTATACCCTCCATTTGATTATTrCTCTT/GT1/ | Primary | |
| RH.DF8645D2839649BZ0Z.R | /rhSeq-r/CTTCACATATAATTTTAAGCTTTTCCATrATTTC/GT1/ | Primary | |
| RH.20D4370B5668462Z0Z.R | /rhSeq-r/AGCACCAATGCATACATTAATAAAArGTGAC/GT4/ | Primary | |
| RH.2A4E2CF43E434E5Z0Z.R | /rhSeq-r/TAGTATATATAGGAAGTAGAGCAAAGGArGATGA/GT1/ | Primary | |
| RH.56288DD4BDA2437Z0Z.R | /rhSeq-r/GCAACAATGAGAAAATGAATTTGCArCAAAA/GT2/ | Primary | |
| RH.E0A3D130866C4EBZ0Z.R | /rhSeq-r/CTTTCCATACGATAAGTACATATCTGArCTTCC/GT4/ | Primary | |
| RH.5F8779D16F6B4D1Z0Z.R | /rhSeq-r/TCCACTTATTTTATAACGATCACTCATrGTGGT/GT3/ | Primary | |
| RH.052C82782DD94B4Z0Z.R | /rhSeq-r/GTTTCAATATCCATCATATCATCAACAATrAATAT/GT2/ | Primary | |
| RH.66FC5A65D6224F4Z0Z.R | /rhSeq-r/TCACAAAACACATTTCATTAGAGGrCATCA/GT1/ | Primary | |
| RH.05877E4991BC46EZ0Z.R | /rhSeq-r/CTCATCTAGTCAATATGAAAATAATATGArGCGTT/GT4/ | Primary | |
| RH.0D67565F4C3847CZ0Z.R | /rhSeq-r/GCAATGATAATACTTGAAGAAAGGTTAArATACC/GT2/ | Primary | |
| RH.1C412A6096B24B6Z0Z.R | /rhSeq-r/CTGATTACCAGATAGGTGAACATAATArATATG/GT3/ | Primary | |
| RH.DADD4A1EC493407Z0Z.R | /rhSeq-r/GGCATATCATTTACATTATCCACAGTTTrCTTTG/GT1/ | Primary | |
| RH.131BA01846444AFZ0Z.R | /rhSeq-r/TTCCAGTAGTTCTTGTAAGACCTATrGAAGG/GT3/ | Primary | |
| RH.2A936B6612214C0Z0Z.R | /rhSeq-r/CTGGGAAAATAAGCTATCATTTTGTAGrAAATG/GT1/ | Primary | |
| RH.77FE64C8830A46AZ0Z.R | /rhSeq-r/TTTCCTCATCATCGTCATTTTCATCArCCAAC/GT4/ | Primary | |
| RH.63B2C6ECC87D409Z0Z.R | /rhSeq-r/GGGCGAAATTCTATGAATGTATTATTrAATAG/GT4/ | Primary | |
| RH.73E1E039A8E1486Z0Z.R | /rhSeq-r/TTTCTTCTCAGATTCGATTTGGACTrATTAC/GT4/ | Primary | |
| RH.9A45E2C5DDFB41FZ0Z.R | /rhSeq-r/GTTGAGTGATAAACCTGCTTATCTTrCATGA/GT2/ | Primary | |
| RH.741CE999A6054F5Z0Z.R | /rhSeq-r/CCATCTCTAGGTAATAACGTACCATTArGAAGA/GT1/ | Primary | |
| RH.AC0C4ED33EB8436Z0Z.R | /rhSeq-r/TAACGTATTTATTAGAGAAGGTTCGGrGTGTG/GT1/ | Primary | |
| RH.D9EE34B6F40F4D4Z0Z.R | /rhSeq-r/CTAAAGCTTCAACGAATGTAAATGTATrCACTA/GT3/ | Primary | |
| RH.A35B05759EF241AZ0Z.R | /rhSeq-r/GTAGAAGGAATAGATACACCATCCTrCTTCA/GT1/ | Primary | |
| RH.00861D1F91E04CEZ0Z.R | /rhSeq-r/TCAGCTAAGCTTAATTTGTTCTCATrCCTTT/GT1/ | Primary | |
| RH.7AFA5825BCFF48CZ0Z.R | /rhSeq-r/AATGGTTGTGTTGAAGAGGTACATAArCTGTA/GT2/ | Primary | |
| RH.3FFB4791AAB740BZ0Z.R | /rhSeq-r/GGTTGGTGTAGATAGACATTTATTGAArCAAAT/GT1/ | Primary | |
| RH.0909F225F86B448Z0Z.R | /rhSeq-r/CAAAACGACGTTATTACAATAATCTTTTrCTGAC/GT4/ | Primary | |
| RH.E89C0AE29BF4491Z0Z.R | /rhSeq-r/CTTATGGTTTCGTCAACAGTATGAAArCGAAT/GT4/ | Primary | |
| RH.DEFD198774AA4F7Z0Z.R | /rhSeq-r/TGTGTTATGTGAAGAAGAAAATATGATTrACACA/GT1/ | Primary | |
| RH.1237EDEE873F4BFZ0Z.R | /rhSeq-r/CAATCTAAAAATGAACAAGAGATATCAACrACAAG/GT2/ | Primary | |
| RH.013BA341493646EZ0Z.R | /rhSeq-r/GTGCAAAATGATCCAATAGACGArCACAT/GT3/ | Primary | |
| RH.125DEC55F816487Z0Z.R | /rhSeq-r/CATCTATAGCAGCAAACTTACTAACArCGTTT/GT3/ | Primary | |
| RH.75608D9B4B37452Z0Z.R | /rhSeq-r/CAACAGAAAATCATATACATACATACACrATATC/GT4/ | Primary | |
| RH.234D1D1718AE438Z0Z.R | /rhSeq-r/TGCTTCCGTACTTTTGTTAGATAArCGTAA/GT2/ | Primary | |
| RH.A2EEDF3F7C3C489Z0Z.R | /rhSeq-r/CACAATAACTTGCAACAGTTCTTATTCrCCATT/GT4/ | Primary | |
| RH.084717DAABF3455Z0Z.R | /rhSeq-r/AAAAAGTTTGTTGATGAAAGAAAGGATrATTGA/GT1/ | Primary | |
| RH.FC2A8FBE072E409Z0Z.R | /rhSeq-r/GAAATTATCCCTCTCTATCTCATCTTrCATTC/GT1/ | Primary | |
| RH.474DC1ABE955486Z0Z.R | /rhSeq-r/TGAAGGATTAAGGAAAGACAGCArACAAT/GT4/ | Primary | |
| RH.0D3AB1C35D2C45EZ0Z.R | /rhSeq-r/TCCATATCCTGGTTGTTCATTArCCAAA/GT2/ | Primary | |
| RH.34536B047B76468Z0Z.R | /rhSeq-r/TTTTGTTCATTCAACACTTGAGCTrATTTT/GT1/ | Primary | |
| RH.3D49C933215B47CZ0Z.R | /rhSeq-r/CATTTCAAGACTTTGAGTTTCTTGATrGAGTA/GT4/ | Primary | |
| RH.8FBEEDC5DA7144EZ0Z.R | /rhSeq-r/GCAAAATCAATATATGAACGAACTGGArCAAGA/GT4/ | Primary | |
| RH.BBAD704FF905480Z0Z.R | /rhSeq-r/GTAACTCTTCAATTCCATCTCTCAAGTArCATTT/GT3/ | Primary | |
| RH.31A583D2771B455Z0Z.R | /rhSeq-r/GTTCACGCTTTTCCTTAATTGTATTGTrCGTTA/GT3/ | Primary | |
| RH.D222DAB4B6474B5Z0Z.R | /rhSeq-r/GATGATTGCATACTTCAAAATGATCrCGTTG/GT4/ | Primary | |
| RH.391355D65D9E4C4Z0Z.R | /rhSeq-r/TGTGTCTGTATTTAATAAATGATTATCTrGGGTT/GT4/ | Primary | |
| RH.B50875B83BA8432Z0Z.R | /rhSeq-r/AAGATCAAGCATTTGTCTGTCTATrATCTC/GT1/ | Primary | |
| RH.F28E178506994BFZ0Z.R | /rhSeq-r/TCCTATGTAGAAATAATACAATTGTCAGrGACAC/GT2/ | Primary | |
| RH.3A58F1684211457Z0Z.R | /rhSeq-r/GATTTTCTCTGTCTTTCAAAATAGCTArATTCA/GT1/ | Primary | |
| RH.627F76C560224A6Z0Z.R | /rhSeq-r/TATCCCTATCTCGAATACTATCCCTGrCGTCT/GT1/ | Primary | |
| RH.72697B5F4E304E6Z0Z.R | /rhSeq-r/GTAGAAGAATTTATGGAAAGGATCTACTTrAAGAA/GT1/ | Primary | |
| RH.B7D7C030BE2C432Z0Z.R | /rhSeq-r/CTCAGATAACATAGCTTCCCAAArGTTTC/GT1/ | Primary | |
| RH.68BE559FDD564A3Z0Z.R | /rhSeq-r/TGATTAGAGTCCTCATTTGCATTrCTGTG/GT4/ | Primary | |
| RH.5193318E754A417Z0Z.R | /rhSeq-r/ACCTAGAAGAAATAATTGTGGTGTTArCGTCA/GT4/ | Primary | |
| RH.46659BEDBC00438Z0Z.R | /rhSeq-r/AACAGATGAAGTAACTACTCGATTAAATrGATCA/GT4/ | Primary | |
| RH.153CD64285C0471Z0Z.R | /rhSeq-r/CCAACATTTCAGGTACATCTTCAAATArATTCA/GT1/ | Primary | |
| RH.98F4419B5559408Z0Z.R | /rhSeq-r/TTCTATATCAGGAGTTCCAGGAGrCAGCT/GT2/ | Primary | |
| RH.654F6CF05F274F6Z0Z.R | /rhSeq-r/GATAATGTATACTCTCACATATTCCCTTrCAGTG/GT1/ | Primary | |
| RH.64BEC91228CA4FEZ0Z.R | /rhSeq-r/CTTGCCCTTTCTCTAATTTGTTCATTATrCATCA/GT4/ | Primary | |
| RH.904F67856AF2484Z0Z.R | /rhSeq-r/GACATGTGTGCTTTGTCGTTGATTrCATTT/GT1/ | Primary | |
| RH.0BF6BBF4558B415Z0Z.R | /rhSeq-r/TCATTTTATCCCACTTATTTATCTCGTrCTTCC/GT1/ | Primary | |
| RH.B8439DE2510B4D4Z0Z.R | /rhSeq-r/TTCTGGGATACTTATATCATCAGTATTTrACGTT/GT1/ | Primary | |
| RH.3792106A3B37488Z0Z.R | /rhSeq-r/ACACTGACATGGTAAATAACGATrAATCA/GT4/ | Primary | |
| RH.90ABC72D97AC491Z0Z.R | /rhSeq-r/AGGAATTCTTATGGAACAAAATTCGAATrCAGGA/GT1/ | Primary | |
| RH.C3822EB7E8094CDZ0Z.R | /rhSeq-r/GGGACAATTAACTTGTCGTATrATATC/GT4/ | Primary | |
| RH.DE684B76F521431Z0Z.R | /rhSeq-r/GTTGTGAGTTTCGGATGTTACArAAACT/GT4/ | Primary | |
| RH.DC31D3E7CDF041EZ0Z.R | /rhSeq-r/CCATTTAATCCTGATAGAATAGCAAATrATTTC/GT4/ | Primary | |
| RH.CB5AE1573D5D439Z0Z.R | /rhSeq-r/TCCTTCATATTTTCTTTTTGATATCCTATrATGAA/GT1/ | Primary | |
| RH.C8EC2CED2C9B4DAZ0Z.R | /rhSeq-r/GATGTGTAATAATGTGTTATATGGAAGArAAAGA/GT1/ | Primary | |
| RH.C1E1BF8D6809480Z0Z.R | /rhSeq-r/TTGCATCATCATTGTCTAAAGCTTrCGTTC/GT1/ | Primary | |
| RH.4188BDD618CA401Z0Z.R | /rhSeq-r/TGGTAGCAATTCTATAAATTGGTTArATTGT/GT1/ | Primary | |
| RH.A33E8496E4FC488Z0Z.R | /rhSeq-r/CCATTACTTATGGGAAGTTTCGGTArATTTC/GT4/ | Primary | |
| RH.ADA7632A77F2409Z0Z.R | /rhSeq-r/GATTGTTCATATCTTCATTATTATGATTrATCAC/GT3/ | Primary | |
| RH.F2DA4EADF4644AAZ0Z.R | /rhSeq-r/TACTCCTTAGGTAAATTAAACGTGTGATrAAAAT/GT4/ | Primary | |
| RH.A79623D3D0BA4D4Z0Z.R | /rhSeq-r/ATCCATAGCAGAGTCTTCTTATTTCTTrATATA/GT4/ | Primary | |
| RH.130807648D6D4A0Z0Z.R | /rhSeq-r/TGAAAATTATATTTCGACCTGCTTCAATrGCATT/GT3/ | Primary | |
| RH.0A4FC70E2BA842CZ0Z.R | /rhSeq-r/CCACGAAAAGGGATAAATATGATGTTrATACA/GT4/ | Primary | |
| RH.C49AA0D57A3A410Z0Z.R | /rhSeq-r/GAGGAAAAACTGAAGAAGTAATGGrGACAT/GT4/ | Primary | |
| RH.F6918FA0DE0E46BZ0Z.R | /rhSeq-r/CATTTCTTACACAAAGCAAAATTATCACrATATG/GT1/ | Primary | |
| RH.E9048996E241498Z0Z.R | /rhSeq-r/ATCAATTGATGGTTGCCTTTCGrATTAA/GT1/ | Primary | |
| RH.54525BCEFAE640DZ0Z.R | /rhSeq-r/GGTTTAAATATAGATGCAGAGATTGGTrGATTT/GT3/ | Primary | |
| RH.50101BFA0F6142AZ0Z.R | /rhSeq-r/GAATCCCCATAAAGCTGCATTTArCAATA/GT4/ | Primary | |
| RH.90A6B553AA964B7Z0Z.R | /rhSeq-r/GATAGATTTGTAGTTCCACAATCATCTrGGAAT/GT1/ | Primary | |
| RH.CA42B27342E04EEZ0Z.R | /rhSeq-r/TGCATTGTCCTTCAGATTCTTTrATCCT/GT4/ | Primary | |
| RH.59246A4CA5304FEZ0Z.R | /rhSeq-r/CATTCAACGGTCAATTTGCTATATTAGrCTGGT/GT2/ | Primary | |
| RH.6302E667853A4ECZ0Z.R | /rhSeq-r/CACAAAAATGTATATTCCAACAAACACrATACA/GT1/ | Primary | |
| RH.1E3DF893CA764FEZ0Z.R | /rhSeq-r/TCAATATGTTTCACATATCTTGCAATCrCATCT/GT1/ | Primary | |
| RH.48A63D3D7846478Z0Z.R | /rhSeq-r/GGACACAATTACGACATAAATAGGTrATTAG/GT2/ | Primary | |
| RH.8D667234A62A4DFZ0Z.R | /rhSeq-r/GAAAATTATTAGAAGAACATCCAAATGArAGAAG/GT4/ | Primary | |
| RH.1E5857F6734342DZ0Z.R | /rhSeq-r/CATGATGCCACATTTTAGTAGTATTATArGATGT/GT4/ | Primary | |
| RH.9DBEDAA38D9D4A7Z0Z.R | /rhSeq-r/GTTAAGTGGAACCTTTTCCAAAATrGGAAG/GT4/ | Primary | |
| RH.AE16A161DEEF472Z0Z.R | /rhSeq-r/TTCTGAAGGACTATATATGGAACAATTrCATTC/GT1/ | Primary | |
| RH.0E85C0E0F5434A6Z0Z.R | /rhSeq-r/CATTATAGATGGAAAGCAACCTACArACGAT/GT4/ | Primary | |
| RH.414A94632E804D2Z0Z.R | /rhSeq-r/CCAATGTTGTATTGTTACTAGTATATACrATCGC/GT1/ | Primary | |
| RH.285DF9E0E6EC45AZ0Z.R | /rhSeq-r/TCCATCAAATAAATTTCGGAATTCATCrCTTCA/GT4/ | Primary | |
| RH.D9BA7A7DDA2443CZ0Z.R | /rhSeq-r/TTGGGATACAACCAATTATCTTACArCCAAC/GT4/ | Primary | |
| RH.73818732C84143EZ0Z.R | /rhSeq-r/GAAGCATTTTCTTCTTTTTGTGATrGATGT/GT1/ | Primary | |
| RH.1CA07193BAC44D7Z0Z.R | /rhSeq-r/TCAACGAAAATAAAAGGTTGTTCTTTTrCAAAT/GT1/ | Primary | |
| RH.4178D0F094A242CZ0Z.R | /rhSeq-r/CACCAATCGTTAATCACAAAATTACAArAATCC/GT4/ | Primary | |
| RH.243246A73EA94F4Z0Z.R | /rhSeq-r/CATGTAATAATACTGTGCCCAAGArATTTG/GT2/ | Primary | |
| RH.264EFB3D472D490Z0Z.R | /rhSeq-r/AGGAGATAGTTTACCTGGTTTCCrCATCA/GT3/ | Primary | |
| RH.F462CC064314480Z0Z.R | /rhSeq-r/TACTTGAGGAATTTTTAGGACATTTGATrAGGTT/GT1/ | Primary | |
| RH.0F8E7CF2B5A44F8Z0Z.R | /rhSeq-r/ATGATACGTTGTACCATCATAAACATTTArAATGT/GT4/ | Primary | |
| RH.45D97578522E475Z0Z.R | /rhSeq-r/TTTGATTTTTGCTTTCTCCGTCArAAGCT/GT3/ | Primary | |
| RH.A697335E3F5046EZ0Z.R | /rhSeq-r/GAAACTGTAGATGAAGATGCTCACrCATGT/GT1/ | Primary | |
| RH.F2DC0BDE0240494Z0Z.R | /rhSeq-r/TTGACCATAAAATACCAGAGGACrGGACA/GT1/ | Primary | |
| RH.DA3C260CCDD546EZ0Z.R | /rhSeq-r/GAGGAACATTTGATGTTTCCTTATTAACArCTTGA/GT4/ | Primary | |
| RH.345B0264CAD84F1Z0Z.R | /rhSeq-r/CATGATGAATATTGTCGTGCTGATrCATCA/GT1/ | Primary | |
| RH.3871A7394354434Z0Z.F | /rhSeq-f/CTTGTATTAAATGGAATACCTCGTTATAGrGATAC/GT1/ | Primary | |
| RH.3871A7394354434Z0Z.R | /rhSeq-r/CCAATAAAAAGTGGATACTCATCATATArCATGT/GT4/ | Primary | |
| RH.38CCFC011FB2480Z0Z.F | /rhSeq-f/CAGAAACTGGTTCAGGGAAAArCCTTA/GT2/ | Secondary | |
| RH.2C3086E2DC5C49AZ0Z.F | /rhSeq-f/GGCTATGGTATCCTTTTTCCAATTrGTTCA/GT3/ | Secondary | |
| RH.DA41F9E31EE74D3Z0Z.F | /rhSeq-f/GATTGCTCCTTTTCTTCACCTTrGGTTT/GT3/ | Secondary | |
| RH.85AB83269724470Z0Z.F | /rhSeq-f/CTCCCCAAAAGTTAACTGCTTCATTrATTTT/GT2/ | Secondary | |
| RH.86C97D8D7E0F4EDZ0Z.F | /rhSeq-f/CAATGGTTGTTATTATTATTATCATCACArATGGT/GT1/ | Secondary | |
| RH.1F52DCDFE637436Z0Z.F | /rhSeq-f/TGATATGTTATTTCATCATCAGCATCGArCTTCT/GT1/ | Secondary | |
| RH.26A0B96A11C849DZ0Z.F | /rhSeq-f/CCAGTTTATCATCTTTAGGCCATAACrCAGAG/GT1/ | Secondary | |
| RH.A7EF0576F3474C1Z0Z.F | /rhSeq-f/ATTGACAAGTTTGTTGATACGATCrGCATC/GT2/ | Secondary | |
| RH.209001BBEA094F0Z0Z.F | /rhSeq-f/CAATGTTGATAATCATTTTAATAACAGCGrCTGCT/GT2/ | Secondary | |
| RH.80FCE3CC97D04DCZ0Z.F | /rhSeq-f/CCGTTGATATAAAAGAAGGATCATTTArCATCC/GT4/ | Secondary | |
| RH.3AB15DABF16A4EFZ0Z.F | /rhSeq-f/TGTGGGTTACTTGTATCATTACAACTrCATCA/GT1/ | Secondary | |
| RH.A543725BF07E4FBZ0Z.F | /rhSeq-f/GATGAAAAGTGTATTGATATCGAACATGTrAGGTA/GT1/ | Secondary | |
| RH.70188AF087D14A3Z0Z.F | /rhSeq-f/TCTTGCCAATTCGATAATATACAAArGAATG/GT1/ | Secondary | |
| RH.CB71A2EB72834B0Z0Z.F | /rhSeq-f/ATAAGCATCATTTTCCTTATCATTATAATrGAGGT/GT1/ | Secondary | |
| RH.68E352C23CEE439Z0Z.F | /rhSeq-f/TTGCTACAAGGAGAAATGACAAATATrGGAGA/GT4/ | Secondary | |
| RH.1DDD6080594D458Z0Z.F | /rhSeq-f/AGAAGAACAAAAACACCCATATCTrAAAGC/GT4/ | Secondary | |
| RH.8FF5E70E99C444DZ0Z.F | /rhSeq-f/GCAGTAATTTTCTAGGTTGTTTCTTGrCTTCA/GT4/ | Secondary | |
| RH.6B7A0019EA0D4CEZ0Z.F | /rhSeq-f/AACATCTACCCTATTACATGTATTGTCrCCCAG/GT3/ | Secondary | |
| RH.B85FB6B913B74A0Z0Z.F | /rhSeq-f/CTGGATTTGGTGAAGGTTCTTGTrGGATT/GT4/ | Secondary | |
| RH.CF51562C1B444DFZ0Z.F | /rhSeq-f/GATTCATTATTCCATTCATCCCAAGAArCATGA/GT4/ | Secondary | |
| RH.0BCB1D973AC3449Z0Z.F | /rhSeq-f/CTATTTTCATAAGAACTGCTTCCATCTrCCTTT/GT3/ | Secondary | |
| RH.184CC47C7EFB49EZ0Z.F | /rhSeq-f/GCTAGAGGCATATAAAGAACTTTTTAAArGTCTT/GT4/ | Secondary | |
| RH.D5AC76D292D8481Z0Z.F | /rhSeq-f/CCATCCTTTTGTTCAAAATAATCACArCGCAA/GT3/ | Secondary | |
| RH.F4AEC19045CD496Z0Z.F | /rhSeq-f/CGTAAATATTTTTCTAACGAACCTTCCrCATGG/GT1/ | Secondary | |
| RH.437B0DFBBF344E8Z0Z.F | /rhSeq-f/AGGATGAAAAACGTTGATACATACAAGArGGAAA/GT2/ | Secondary | |
| RH.A8A6AE5229774EEZ0Z.F | /rhSeq-f/AAGAAATGTTGCTGGATCCTTTTrCTCGA/GT1/ | Secondary | |
| RH.0F6F2BC51C1E4D1Z0Z.F | /rhSeq-f/ACGTTACACTTCTTAAAGCAGTrAATTG/GT4/ | Secondary | |
| RH.A05016C7FADC4FAZ0Z.F | /rhSeq-f/GGTATACTCTATATAATTCGTCTCTGTTrCATTC/GT1/ | Secondary | |
| RH.BAD01846F3F64D6Z0Z.F | /rhSeq-f/GTTTAAAAGATATGGCTGCAAAAAGGrGACAA/GT1/ | Secondary | |
| RH.429434A4255D409Z0Z.F | /rhSeq-f/GAGATGTAAATGCACACATTGTAGrGTGCT/GT3/ | Secondary | |
| RH.960A0EA63212444Z0Z.F | /rhSeq-f/CACAATTATAACATCTATCACTACATGGrGCTTC/GT3/ | Secondary | |
| RH.BD0F58D84BEB443Z0Z.F | /rhSeq-f/CCTCCGATTGGTAGTTATACAGArAACCA/GT4/ | Secondary | |
| RH.F8E1C77C5D524A7Z0Z.F | /rhSeq-f/CTTGTAATAATGTAACTGATGCTAATAGTrATGAA/GT4/ | Secondary | |
| RH.ECC7CB7BA56E483Z0Z.F | /rhSeq-f/CATCCTTTATTTCAACAGACTTAAGATrGATCA/GT1/ | Secondary | |
| RH.B8D73E57A1B24E7Z0Z.F | /rhSeq-f/CCACCTAAATTGTTAACATTAGAAGTATTrATTTG/GT1/ | Secondary | |
| RH.6F917D4CEC604E1Z0Z.F | /rhSeq-f/GTTTTCCATCCGATTCTGCATrGCAGT/GT4/ | Secondary | |
| RH.B23FFA445FC94E2Z0Z.F | /rhSeq-f/GTCCTTTTGCATTTTTGCTACArCAAGT/GT1/ | Secondary | |
| RH.FFC40114FD414C8Z0Z.F | /rhSeq-f/ACACTTCAACTACACTTTTTAATTTAGCrCCATA/GT3/ | Secondary | |
| RH.6697958595E04DFZ0Z.F | /rhSeq-f/CCAAAGTAATAACATTCAAAATTTTTCATrCGCAG/GT2/ | Secondary | |
| RH.01C102B54E6944CZ0Z.F | /rhSeq-f/CCATTTCGATAATAGCTGCAGrCGGGT/GT2/ | Secondary | |
| RH.60EC2A7464B6458Z0Z.F | /rhSeq-f/CCCAGATGACAATTATTACCATCATrCAACA/GT1/ | Secondary | |
| RH.17A44B5FAE244B3Z0Z.F | /rhSeq-f/TGTCCCTCTAGTAGAGTGGAArCAAAC/GT4/ | Secondary | |
| RH.64702A0DFE49498Z0Z.F | /rhSeq-f/CATTTACATATAACTCCAACTCCTTTTArCAACA/GT1/ | Secondary | |
| RH.3189B461B55849BZ0Z.F | /rhSeq-f/TTTATTGGCTTACATAACGTGTTGAAArATATT/GT1/ | Secondary | |
| RH.EF10A57CA994425Z0Z.F | /rhSeq-f/TACGATTCAGTTATTTCAGTATGAGTTTrCAACA/GT2/ | Secondary | |
| RH.C3760B64710B45EZ0Z.F | /rhSeq-f/AAGAGGACAGAATTATTGGGAACATrCCATA/GT1/ | Secondary | |
| RH.BA30F88265A946DZ0Z.F | /rhSeq-f/GATCCTCTTCACTTCCCTTCATATrCTTTT/GT2/ | Secondary | |
| RH.2D958A608CCB49BZ0Z.F | /rhSeq-f/ACAAAATCTGCATCTTTTATTACATCGTrAAAAA/GT2/ | Secondary | |
| RH.9CF4B8102046403Z0Z.F | /rhSeq-f/GCATACATTCTATTAAAAACTTTGGGTArCTCCT/GT4/ | Secondary | |
| RH.5FCACBB1F8574D3Z0Z.F | /rhSeq-f/GATTGCTATAGTCATGATCATCGTCATrGGTAA/GT1/ | Secondary | |
| RH.EC4FD058FF204BFZ0Z.F | /rhSeq-f/GGTACATTATTATGGAAACAGCATATTTrAATAG/GT1/ | Secondary | |
| RH.1EAE08EB1B7C467Z0Z.F | /rhSeq-f/AACCATTCATATTTTCTAGGTTTGTTTrAACCA/GT4/ | Secondary | |
| RH.D95C9C016C1F4C2Z0Z.F | /rhSeq-f/AGTCCAATTGAGAATCCTGGArGAGTT/GT1/ | Secondary | |
| RH.0EED4EF5684A4E3Z0Z.F | /rhSeq-f/TGAAGCTAATTCCTTTCCATATGATrATGGA/GT1/ | Secondary | |
| RH.7F8079FA2E2C4F6Z0Z.F | /rhSeq-f/GTATCAGAACTTGTCGCTATACCTTrCATCT/GT4/ | Secondary | |
| RH.F2A4D3C9F8AB421Z0Z.F | /rhSeq-f/CTCCATAAGTGCTACAGTTATATAGGArCGATT/GT1/ | Secondary | |
| RH.F882EDD7A2C8445Z0Z.F | /rhSeq-f/CATGTAATGCTTCATCAGGTAATGTrCTTCT/GT1/ | Secondary | |
| RH.9348582F6607436Z0Z.F | /rhSeq-f/TCCTTTTATACCTCTTTCTTTCGTrCTTTC/GT1/ | Secondary | |
| RH.3CD61F4A3EC84D9Z0Z.F | /rhSeq-f/CAAGCTGTTGTCACTACCCATArCATTT/GT2/ | Secondary | |
| RH.4032AF467C94419Z0Z.F | /rhSeq-f/TGATTATTCATAAGTTGTTCAGATGTrCGCAG/GT2/ | Secondary | |
| RH.CC76F5A01AAF4A5Z0Z.F | /rhSeq-f/GGTTACTTTCTGAGGCAGGArAATGA/GT2/ | Secondary | |
| RH.7EF8BA84048C483Z0Z.F | /rhSeq-f/CGAAAACCATTAGTTGAAAATAATGATrGATGG/GT4/ | Secondary | |
| RH.2BEB5EEEA53A46CZ0Z.F | /rhSeq-f/ACCAAAAGAAAATGAAAAAGACAAGArGTACA/GT4/ | Secondary | |
| RH.D077AA69CAD4490Z0Z.F | /rhSeq-f/ATCTTGTCTCATGTCATGTGTArCAATC/GT1/ | Secondary | |
| RH.71DC9851AABE4BFZ0Z.F | /rhSeq-f/GATGAATTATTAAATGCCTTTGATTTTCArCGTAC/GT1/ | Secondary | |
| RH.A52BFE1490C7474Z0Z.F | /rhSeq-f/CCTGTTGTTATGAGAATAAATCCATTTrCAATC/GT1/ | Secondary | |
| RH.02D168BF42AD424Z0Z.F | /rhSeq-f/CGAAGGATTTAAACACGAATCGArGCTTA/GT1/ | Secondary | |
| RH.CB832A6786BA4EDZ0Z.F | /rhSeq-f/TATGCCTTTGTTAATGAAGGAGAAGAArCGTGA/GT4/ | Secondary | |
| RH.10DA1ECD243149BZ0Z.F | /rhSeq-f/GTTTGTTTGGTAAATGACGAAGAArCTAGC/GT1/ | Secondary | |
| RH.3FD2DDF76D5B45EZ0Z.F | /rhSeq-f/AGTTGTTATATTCATGTGCTTTAATATATrCCATG/GT4/ | Secondary | |
| RH.4331D5E19F594F5Z0Z.F | /rhSeq-f/CAGCATGTTTTGTTTTAGACCArGCAAA/GT4/ | Secondary | |
| RH.E2E58B2886E941CZ0Z.F | /rhSeq-f/TGAATACATGAATATGATTAACAACGAArCCCAT/GT4/ | Secondary | |
| RH.585DED59BBCE4B3Z0Z.F | /rhSeq-f/ACCTGCAAGTACCTCAACATrCTGAA/GT1/ | Secondary | |
| RH.43611B63CEA141FZ0Z.F | /rhSeq-f/GCACCGATTTTCTATATGTAGCAATTTrCCGAA/GT1/ | Secondary | |
| RH.D583E7EF3B834BDZ0Z.F | /rhSeq-f/ATTTAGAAAACAATTTGAAAAGTGTGGrCAACA/GT3/ | Secondary | |
| RH.DFF26DD6D5874AEZ0Z.F | /rhSeq-f/ATAGGAAAATTAATGGATGTGATTTCTrCTACG/GT4/ | Secondary | |
| RH.B25A5029099243CZ0Z.F | /rhSeq-f/ATTTTTCCAATTTTGGTTTTATGCGrCAGAA/GT4/ | Secondary | |
| RH.BD9F0282F8BC44FZ0Z.F | /rhSeq-f/AAGAAACTGTGGATAATGTAAATGATATrGCCTA/GT4/ | Secondary | |
| RH.A45404EA4014445Z0Z.F | /rhSeq-f/GACACTATCTTTATGATCTATTGGTATGrGCATG/GT4/ | Secondary | |
| RH.8880BEB63BF345FZ0Z.F | /rhSeq-f/GTAGAATATCAAAAGAAATTCGTAACATrAAAGA/GT1/ | Secondary | |
| RH.CA097C50AD13498Z0Z.F | /rhSeq-f/ATCTGGCTCTGTAACCATGTrCCGAA/GT3/ | Secondary | |
| RH.69B864574E3E4F2Z0Z.F | /rhSeq-f/AAAGAAAAGTTAAATAAGGAAAACCAArAAGAG/GT4/ | Secondary | |
| RH.1C97F6677B1A4F1Z0Z.F | /rhSeq-f/GAACTTCGCCATTTTCTCCTrCCTGT/GT4/ | Secondary | |
| RH.B81CF7923D9E42DZ0Z.F | /rhSeq-f/TTATGAAGACAGAGAAGATGGTGCrGGGTC/GT4/ | Secondary | |
| RH.9DBD0230BC684F0Z0Z.F | /rhSeq-f/GATGGTGACAAAAGAGGTAAAGTrAATTT/GT3/ | Secondary | |
| RH.6F3EEAA437F74D1Z0Z.F | /rhSeq-f/GATTCACATTATCCAAACCCATTTAArCGAGT/GT4/ | Secondary | |
| RH.5B78E38974434BEZ0Z.F | /rhSeq-f/CTTTTATGTATATCGTTTCGATTTAGGTrCTTCC/GT1/ | Secondary | |
| RH.72DCDD683E214A9Z0Z.F | /rhSeq-f/CCATTTGACGTAACACCACAATTrATTTC/GT1/ | Secondary | |
| RH.B718263908D8449Z0Z.F | /rhSeq-f/ACAAAAACATTTTCGTTCTTGTCATATrACAGA/GT1/ | Secondary | |
| RH.84E8B65A2096423Z0Z.F | /rhSeq-f/GTAGTTTCAGTTGTCTCCTTTGTrCGCAG/GT3/ | Secondary | |
| RH.DA0E595014364EBZ0Z.F | /rhSeq-f/GGTATTTTTGTTGAACCTAAACGTGrCTGTT/GT3/ | Secondary | |
| RH.3B8D0EC6F6C6462Z0Z.F | /rhSeq-f/AAGAATTATTATTGTTCGTTTCGTTTGAArATTTC/GT2/ | Secondary | |
| RH.36BDF576C6DB4F8Z0Z.F | /rhSeq-f/CTTTTACCAGCAGTAGAAACTACATTrCTCTC/GT2/ | Secondary | |
| RH.15CF296596B542CZ0Z.F | /rhSeq-f/TAAAGAAGAATGTGGAGCTGATrGTTCG/GT1/ | Secondary | |
| RH.64A471F8114C4EBZ0Z.F | /rhSeq-f/GTTGTCCTTCTTCATTTCATTATAACATArCATTC/GT4/ | Secondary | |
| RH.FCBAC6E61DA6486Z0Z.F | /rhSeq-f/AATTTCACCTAACGGTATATTTTTATCTrCGTAC/GT4/ | Secondary | |
| RH.E2E3675947364F0Z0Z.F | /rhSeq-f/TCTTTTGAAACACAAGAAGAAAATTCTrATCAT/GT4/ | Secondary | |
| RH.41A2E5EDA27E4A6Z0Z.F | /rhSeq-f/CATCATTTTCTGGAATGTACTTATCCrCCTGA/GT1/ | Secondary | |
| RH.B245B70A9556406Z0Z.F | /rhSeq-f/CATTTAGCGAACATATAAACCGAGATrAATGG/GT4/ | Secondary | |
| RH.F1B5DE43984A4C3Z0Z.F | /rhSeq-f/TCTGTGTTTGGTGTAATATTAAAGArACATG/GT4/ | Secondary | |
| RH.7DAE780F6E1F4CEZ0Z.F | /rhSeq-f/TGCAAATTGAGCCATAGAAAAATGATTCTrCATTC/GT3/ | Secondary | |
| RH.9F6A5B24F526464Z0Z.F | /rhSeq-f/CTTGCTTATCCTTATCTAATTGTCCAArGAGCA/GT1/ | Secondary | |
| RH.0DE9625DCED040EZ0Z.F | /rhSeq-f/CATTTAAATTCTCTTTTTCCACAGCTCrCAGCA/GT1/ | Secondary | |
| RH.FD87905E6F6A441Z0Z.F | /rhSeq-f/TTTTTAAAGCATCATTTTGCTCATAATTrATATG/GT1/ | Secondary | |
| RH.C9F428247EFD420Z0Z.F | /rhSeq-f/TACTATTATACCATATGTTGCTGGGTrCGACT/GT1/ | Secondary | |
| RH.CACF522163CE4CAZ0Z.F | /rhSeq-f/TCCTGCAGGTAAATCATGAGTArCTGTG/GT1/ | Secondary | |
| RH.40739B704E25438Z0Z.F | /rhSeq-f/TTGAATCCATGAAATAGGAATATGAATTTrCCAAT/GT4/ | Secondary | |
| RH.BF2C63B8506045BZ0Z.F | /rhSeq-f/GCATGTAAGTTAACAATTTCCAGTrGCTGT/GT4/ | Secondary | |
| RH.D264872CCD7948DZ0Z.F | /rhSeq-f/ACTTATTCTTCCTCTATTTCTACCTTTrGCCTC/GT1/ | Secondary | |
| RH.DBA8DBECAF76495Z0Z.F | /rhSeq-f/TTTAGTTTCGGTATTTTGTGTTCCTrCTTTT/GT3/ | Secondary | |
| RH.818EF134864243BZ0Z.F | /rhSeq-f/TTTATATTTAAAACTGACATGACCAAArAACTG/GT2/ | Secondary | |
| RH.4BBC0342F96D444Z0Z.F | /rhSeq-f/CATTAATATCAATTATTGGTCGACCTAATrGTTGG/GT1/ | Secondary | |
| RH.12FF002BF1B741AZ0Z.F | /rhSeq-f/TGTCTTTGTCTCTTTTCCTTTCTCATATrCAGAT/GT4/ | Secondary | |
| RH.0BCE12D04779446Z0Z.F | /rhSeq-f/CACTCAATTTTGTTAAATCCCTTGTTTTrCTCAA/GT1/ | Secondary | |
| RH.CF43B917AB504FBZ0Z.F | /rhSeq-f/CAGCATGCTAGAGAAGATGGArCAAAC/GT4/ | Secondary | |
| RH.3C58FDC17E81435Z0Z.F | /rhSeq-f/CAACTGGTGTTGCAAAACCATTArGTTAC/GT3/ | Secondary | |
| RH.DA4225345CB143AZ0Z.F | /rhSeq-f/ATGCAACCATACCACCAATTAATAACrCATCA/GT4/ | Secondary | |
| RH.38CCFC011FB2480Z0Z.R | /rhSeq-r/CGCGAGTAGGTTCCAATACTArATATG/GT2/ | Secondary | |
| RH.2C3086E2DC5C49AZ0Z.R | /rhSeq-r/ACTGTGTTTCTTCCCAAGAATAAArCATGC/GT2/ | Secondary | |
| RH.DA41F9E31EE74D3Z0Z.R | /rhSeq-r/GATGACAATTTTGCTCTTGTGAATrGAAAG/GT1/ | Secondary | |
| RH.85AB83269724470Z0Z.R | /rhSeq-r/GAAGCATTATGTGTCTTGTTATCATTGrGCTTT/GT1/ | Secondary | |
| RH.86C97D8D7E0F4EDZ0Z.R | /rhSeq-r/CGTCAGTATATGTTTAATTTAAGTATGAArGGGTG/GT4/ | Secondary | |
| RH.1F52DCDFE637436Z0Z.R | /rhSeq-r/CAAGAAGAGTTATGACAACCAAAATGAArGGAAT/GT2/ | Secondary | |
| RH.26A0B96A11C849DZ0Z.R | /rhSeq-r/GCTTTTGGCTATTTTTAGTTTTATCGCTrACTCT/GT1/ | Secondary | |
| RH.A7EF0576F3474C1Z0Z.R | /rhSeq-r/TCATCACCCCAAAATGAATTTAAArCTTGC/GT4/ | Secondary | |
| RH.209001BBEA094F0Z0Z.R | /rhSeq-r/CCTTTTCCATTTTATATACTTCTTCATCArCATTC/GT1/ | Secondary | |
| RH.80FCE3CC97D04DCZ0Z.R | /rhSeq-r/CTTTTTGTAAGCCACAATTTCATCGrCCTAC/GT3/ | Secondary | |
| RH.3AB15DABF16A4EFZ0Z.R | /rhSeq-r/CGAATCAAATGATTAATGGAGGAGGArAATAA/GT1/ | Secondary | |
| RH.A543725BF07E4FBZ0Z.R | /rhSeq-r/CCATCAAGGGTGTGGTAAAATAATTTTGrCTCTT/GT3/ | Secondary | |
| RH.70188AF087D14A3Z0Z.R | /rhSeq-r/GACATATATGTGTGATAGAGAAAGGTTrCAATT/GT2/ | Secondary | |
| RH.CB71A2EB72834B0Z0Z.R | /rhSeq-r/CAATAGATGTCCCATTACCTAATGATTTArGCATC/GT1/ | Secondary | |
| RH.68E352C23CEE439Z0Z.R | /rhSeq-r/GGATTTTCATATTCATCTGTAGAATCGrGTAAG/GT4/ | Secondary | |
| RH.1DDD6080594D458Z0Z.R | /rhSeq-r/GGTACCCTCTCTAGAATTTGCTrCAAAT/GT2/ | Secondary | |
| RH.8FF5E70E99C444DZ0Z.R | /rhSeq-r/TTGATGCTAATGGTATCCTAAATGTAArCAGCA/GT1/ | Secondary | |
| RH.6B7A0019EA0D4CEZ0Z.R | /rhSeq-r/CAAAATTAGTAAGGCACTACGAAACArGATGT/GT1/ | Secondary | |
| RH.B85FB6B913B74A0Z0Z.R | /rhSeq-r/GTGTAACTTGTGGTAAAGGTACCArGGTCA/GT4/ | Secondary | |
| RH.CF51562C1B444DFZ0Z.R | /rhSeq-r/CTCAGCATAGTACTCAATTAGTTAGTGrGCTTT/GT1/ | Secondary | |
| RH.0BCB1D973AC3449Z0Z.R | /rhSeq-r/CGCATGTAGATTAATATGGAGAAAATTrAAAGA/GT4/ | Secondary | |
| RH.184CC47C7EFB49EZ0Z.R | /rhSeq-r/GTAGAAATCGTCGAAGAACATATACATrAAAAT/GT1/ | Secondary | |
| RH.D5AC76D292D8481Z0Z.R | /rhSeq-r/GGTTCATTTGTTTGAGCAAATTCTTrGAGCA/GT1/ | Secondary | |
| RH.F4AEC19045CD496Z0Z.R | /rhSeq-r/GTTGTTATAATTATTCGTTGGATTCCTrAATAT/GT4/ | Secondary | |
| RH.437B0DFBBF344E8Z0Z.R | /rhSeq-r/CTGGACCTTGTATACAACTAACAATAGTrATATG/GT1/ | Secondary | |
| RH.A8A6AE5229774EEZ0Z.R | /rhSeq-r/ACATGGTTTCTGGATATTCTTGATrAGGTT/GT4/ | Secondary | |
| RH.0F6F2BC51C1E4D1Z0Z.R | /rhSeq-r/CCTCTTTGCGTTACAGAGTTTArCATTA/GT1/ | Secondary | |
| RH.A05016C7FADC4FAZ0Z.R | /rhSeq-r/GAAAAGGAAACAAATAAGGATAAAAACArAAAAA/GT4/ | Secondary | |
| RH.BAD01846F3F64D6Z0Z.R | /rhSeq-r/ATATCTTCCATGACAAGGAAGAATTATrAATCG/GT1/ | Secondary | |
| RH.429434A4255D409Z0Z.R | /rhSeq-r/TAGGATTCAGCCATTTCGATAATAGrCAGCA/GT2/ | Secondary | |
| RH.960A0EA63212444Z0Z.R | /rhSeq-r/GTAGAAGTAAAGGTTTACAACTTTCTCrCTAGC/GT4/ | Secondary | |
| RH.BD0F58D84BEB443Z0Z.R | /rhSeq-r/AAGGAGATGTATCATTTGCACGAArCTCCT/GT1/ | Secondary | |
| RH.F8E1C77C5D524A7Z0Z.R | /rhSeq-r/GTTCATTATATAATCCAATTGTCTGATTrCCACA/GT4/ | Secondary | |
| RH.ECC7CB7BA56E483Z0Z.R | /rhSeq-r/GTCCATTGGATTTAATTCCTCTATATATrCTTAC/GT3/ | Secondary | |
| RH.B8D73E57A1B24E7Z0Z.R | /rhSeq-r/AACGATATTCTAAACTGCATTCAGAATTCrCTCCA/GT4/ | Secondary | |
| RH.6F917D4CEC604E1Z0Z.R | /rhSeq-r/GAGAAAATATGCTGCCACTAAACrGTAGC/GT4/ | Secondary | |
| RH.B23FFA445FC94E2Z0Z.R | /rhSeq-r/GCCTCCGTACTTTTGTTAGATAACrGTAAG/GT3/ | Secondary | |
| RH.FFC40114FD414C8Z0Z.R | /rhSeq-r/GAGATTTAACTTTACATCATTGTACACArACATT/GT1/ | Secondary | |
| RH.6697958595E04DFZ0Z.R | /rhSeq-r/CCCTTCATATAATTTTTGGTATTACATTrCTGAT/GT2/ | Secondary | |
| RH.01C102B54E6944CZ0Z.R | /rhSeq-r/GAGATGTGAATGCACTTATTGTrCGGTG/GT3/ | Secondary | |
| RH.60EC2A7464B6458Z0Z.R | /rhSeq-r/CATGAATTTGTATCATCATTCTTCAATrGAATG/GT1/ | Secondary | |
| RH.17A44B5FAE244B3Z0Z.R | /rhSeq-r/GATGAAGAAGTGGAAGGCATrATTTG/GT4/ | Secondary | |
| RH.64702A0DFE49498Z0Z.R | /rhSeq-r/TTTTAAATTGTGGAAAAGGTGTTTGTrAAGAA/GT1/ | Secondary | |
| RH.3189B461B55849BZ0Z.R | /rhSeq-r/TAACTCATGTGCTACTTCATCTTTGTrCTTTT/GT1/ | Secondary | |
| RH.EF10A57CA994425Z0Z.R | /rhSeq-r/TGTATTGAGAATTGTACAAACACAGAACrCAATA/GT2/ | Secondary | |
| RH.C3760B64710B45EZ0Z.R | /rhSeq-r/TGAAAATAAATTTTGTTCTTGTGGTGCrGGGTT/GT3/ | Secondary | |
| RH.BA30F88265A946DZ0Z.R | /rhSeq-r/GAAGATAGGGCTACTAAATTGAGGGrATTTA/GT4/ | Secondary | |
| RH.2D958A608CCB49BZ0Z.R | /rhSeq-r/GGAAAAAGATACAAATATAACATACCCTTrGGTAT/GT2/ | Secondary | |
| RH.9CF4B8102046403Z0Z.R | /rhSeq-r/AGGAATTTGTATAATGGTGTAATACCTrGCATG/GT1/ | Secondary | |
| RH.5FCACBB1F8574D3Z0Z.R | /rhSeq-r/CATTTGAATCATATGTGTTACCTGGArGATTC/GT4/ | Secondary | |
| RH.EC4FD058FF204BFZ0Z.R | /rhSeq-r/TCTTATAAATATTATATGCAACACCCArCCATT/GT1/ | Secondary | |
| RH.1EAE08EB1B7C467Z0Z.R | /rhSeq-r/GACGAAATTTATGAAGATGAGCAATTTTrGCTTA/GT1/ | Secondary | |
| RH.D95C9C016C1F4C2Z0Z.R | /rhSeq-r/CACCTATTAAATGAGGACCCAGrATCAT/GT1/ | Secondary | |
| RH.0EED4EF5684A4E3Z0Z.R | /rhSeq-r/TTCTCTATCTTCTTGTCCTTTTGATrGGGTT/GT4/ | Secondary | |
| RH.7F8079FA2E2C4F6Z0Z.R | /rhSeq-r/AGAGTCAAGTTTTGTTCAGAAGGATTrATTGG/GT1/ | Secondary | |
| RH.F2A4D3C9F8AB421Z0Z.R | /rhSeq-r/AACTTAAAAATGAGGACAAGGAAAATrAATAC/GT4/ | Secondary | |
| RH.F882EDD7A2C8445Z0Z.R | /rhSeq-r/TGGTGTGTTTTGATCATTTCCATTrATTCA/GT4/ | Secondary | |
| RH.9348582F6607436Z0Z.R | /rhSeq-r/TGGGAACATACCATCTAATACAAArCATGA/GT2/ | Secondary | |
| RH.3CD61F4A3EC84D9Z0Z.R | /rhSeq-r/AAACGCTACAGTAGAGCAAACAArAAGAA/GT4/ | Secondary | |
| RH.4032AF467C94419Z0Z.R | /rhSeq-r/AAAGTTACAGAGGAGAAGAAAAAGArCACCT/GT1/ | Secondary | |
| RH.CC76F5A01AAF4A5Z0Z.R | /rhSeq-r/CTCATTGGGACGGATTGGTCrCGAAA/GT2/ | Secondary | |
| RH.7EF8BA84048C483Z0Z.R | /rhSeq-r/TCATTTACAATAATATCTCCTTCGGTTrGGATC/GT4/ | Secondary | |
| RH.2BEB5EEEA53A46CZ0Z.R | /rhSeq-r/GAAACACCAAAACCAGCTATTTCTTrGATAT/GT2/ | Secondary | |
| RH.D077AA69CAD4490Z0Z.R | /rhSeq-r/CAGCTTCTATACCTAATGCTTGTrAAACT/GT4/ | Secondary | |
| RH.71DC9851AABE4BFZ0Z.R | /rhSeq-r/CATGTTTAAATGCTTTTGTATTTTCAGTTrGTCCT/GT1/ | Secondary | |
| RH.A52BFE1490C7474Z0Z.R | /rhSeq-r/TCTGAGTTTATATTAGGAACATTTGTrAACAT/GT1/ | Secondary | |
| RH.02D168BF42AD424Z0Z.R | /rhSeq-r/ATTTCCTCTCTCACAATACTCCATrCAACA/GT1/ | Secondary | |
| RH.CB832A6786BA4EDZ0Z.R | /rhSeq-r/GGTTTTGTTTCAATTTTTCTTGGTGGTrATGGA/GT4/ | Secondary | |
| RH.10DA1ECD243149BZ0Z.R | /rhSeq-r/GAATCATTTTCATTATTATTCTCATCCACrATTTT/GT1/ | Secondary | |
| RH.3FD2DDF76D5B45EZ0Z.R | /rhSeq-r/CTCAAATGTTCTAGAAAATATGACArGGTCT/GT1/ | Secondary | |
| RH.4331D5E19F594F5Z0Z.R | /rhSeq-r/GTTTAGGTTGATCCGAAGCArCTCAA/GT1/ | Secondary | |
| RH.E2E58B2886E941CZ0Z.R | /rhSeq-r/CAAGCTGAAAACATATAATAATCTTGAArCCCTC/GT1/ | Secondary | |
| RH.585DED59BBCE4B3Z0Z.R | /rhSeq-r/GCACAGTAGCACCATTATGTrGATCA/GT1/ | Secondary | |
| RH.43611B63CEA141FZ0Z.R | /rhSeq-r/CGTCATCAACAAATATTTTCGAATCAGrCGCTA/GT1/ | Secondary | |
| RH.D583E7EF3B834BDZ0Z.R | /rhSeq-r/AGATGGGTCTTCATTATTATTATTAACATrCATGG/GT1/ | Secondary | |
| RH.DFF26DD6D5874AEZ0Z.R | /rhSeq-r/CATGAAAACATTTTTCTGGATCTAArATTTG/GT1/ | Secondary | |
| RH.B25A5029099243CZ0Z.R | /rhSeq-r/ACAAATATTGGTGTATGTACAGGTrAGAAA/GT2/ | Secondary | |
| RH.BD9F0282F8BC44FZ0Z.R | /rhSeq-r/TCCCAAGTAAAACTATTAGATCTTCAArCTTTG/GT1/ | Secondary | |
| RH.A45404EA4014445Z0Z.R | /rhSeq-r/GTGATGAATACTAATAGTAGTGGTAGGrAGAAC/GT4/ | Secondary | |
| RH.8880BEB63BF345FZ0Z.R | /rhSeq-r/GCACAATAATGGAAAAAGAAAATGCArATTAT/GT4/ | Secondary | |
| RH.CA097C50AD13498Z0Z.R | /rhSeq-r/CCCCAACGTTTCTTCGATCrAAATG/GT4/ | Secondary | |
| RH.69B864574E3E4F2Z0Z.R | /rhSeq-r/TCCAAATTTCCCTTTACTGTATTTTCrCTCCA/GT1/ | Secondary | |
| RH.1C97F6677B1A4F1Z0Z.R | /rhSeq-r/GAAGCTAGAAGTTCAGGAGCArGCTTT/GT1/ | Secondary | |
| RH.B81CF7923D9E42DZ0Z.R | /rhSeq-r/ATTACCCGCTGATGATACTTGTGrCACGA/GT4/ | Secondary | |
| RH.9DBD0230BC684F0Z0Z.R | /rhSeq-r/ACACTGTGTATTTTGGATACAATGrGGTCC/GT3/ | Secondary | |
| RH.6F3EEAA437F74D1Z0Z.R | /rhSeq-r/TGACATAATAATATCGTTTTTGGATTGTrATCCA/GT4/ | Secondary | |
| RH.5B78E38974434BEZ0Z.R | /rhSeq-r/GAGAGGTATGTTAGGTAAAGAAAATACTrCACCA/GT4/ | Secondary | |
| RH.72DCDD683E214A9Z0Z.R | /rhSeq-r/GCGTATGTGTACACCTATGTCTArCCAAA/GT4/ | Secondary | |
| RH.B718263908D8449Z0Z.R | /rhSeq-r/CTTCCTCCCTGATAAATTTCTTTTGTArCTTGT/GT1/ | Secondary | |
| RH.84E8B65A2096423Z0Z.R | /rhSeq-r/TTGGTTTAAACGCTTTGAATGGTrGTTCC/GT4/ | Secondary | |
| RH.DA0E595014364EBZ0Z.R | /rhSeq-r/CAATACTTATAATTGGTTTCGCATCArCATTT/GT3/ | Secondary | |
| RH.3B8D0EC6F6C6462Z0Z.R | /rhSeq-r/CTCATCATCATTATATACAACAGCAGTTArGTGGA/GT1/ | Secondary | |
| RH.36BDF576C6DB4F8Z0Z.R | /rhSeq-r/GTTTTAAATAGTACAGTTGAAGAAGGTrGATGA/GT4/ | Secondary | |
| RH.15CF296596B542CZ0Z.R | /rhSeq-r/CTGCAAGTTTAAAACGGAACGrGCAAG/GT2/ | Secondary | |
| RH.64A471F8114C4EBZ0Z.R | /rhSeq-r/GAATCCATTGTTATACTTTATCAAAAGArGGAGT/GT1/ | Secondary | |
| RH.FCBAC6E61DA6486Z0Z.R | /rhSeq-r/TCTTTATGTATTTTTCAAAAATCGGCArCGTTT/GT3/ | Secondary | |
| RH.E2E3675947364F0Z0Z.R | /rhSeq-r/CTATTTCCCTTGTCATGTTTGAAAAGrCATAC/GT4/ | Secondary | |
| RH.41A2E5EDA27E4A6Z0Z.R | /rhSeq-r/AAAAGGAACAATGTAATGGTTGAAAArGGATT/GT4/ | Secondary | |
| RH.B245B70A9556406Z0Z.R | /rhSeq-r/GGATTCCATATATGTACAAGAACTCCArCAAGT/GT4/ | Secondary | |
| RH.F1B5DE43984A4C3Z0Z.R | /rhSeq-r/TTAGATCCAGGATTATTATCATGAAATTrGTCCA/GT1/ | Secondary | |
| RH.7DAE780F6E1F4CEZ0Z.R | /rhSeq-r/GCGATAACACTAGATGTAAGATATGCATrCATGT/GT4/ | Secondary | |
| RH.9F6A5B24F526464Z0Z.R | /rhSeq-r/GAAACAAAGAACATTAGAAGCTACTCArGAAAC/GT1/ | Secondary | |
| RH.0DE9625DCED040EZ0Z.R | /rhSeq-r/GAAGATGATGAAATGTATGATGATATGGArAGATG/GT4/ | Secondary | |
| RH.FD87905E6F6A441Z0Z.R | /rhSeq-r/GTTCATATATATAATTCAACAACAGCCArGTTTA/GT1/ | Secondary | |
| RH.C9F428247EFD420Z0Z.R | /rhSeq-r/GAGACCATATCAAATGAACTTGTCArGTGTT/GT1/ | Secondary | |
| RH.CACF522163CE4CAZ0Z.R | /rhSeq-r/TGGGTGAAGGAACTCATAGTGrCAGTG/GT3/ | Secondary | |
| RH.40739B704E25438Z0Z.R | /rhSeq-r/TCAGCAACGATAGTACAAATTGAATGATrGAATG/GT2/ | Secondary | |
| RH.BF2C63B8506045BZ0Z.R | /rhSeq-r/GATGTAAATGCACTTATTGTTGCTGrCACAT/GT2/ | Secondary | |
| RH.D264872CCD7948DZ0Z.R | /rhSeq-r/GAAGATGAAGATGATGAATATTCCATAArGTGAT/GT2/ | Secondary | |
| RH.DBA8DBECAF76495Z0Z.R | /rhSeq-r/TTATCAGAGTTACAAAAGGGAAATCAArCCTTG/GT3/ | Secondary | |
| RH.818EF134864243BZ0Z.R | /rhSeq-r/TCTAGCGAATAATCTTTTTAAAAArACTGG/GT4/ | Secondary | |
| RH.4BBC0342F96D444Z0Z.R | /rhSeq-r/GATGATTCTTTTAGAGCCATAAGAATTTrGATCC/GT1/ | Secondary | |
| RH.12FF002BF1B741AZ0Z.R | /rhSeq-r/TCAGTCTATAAATCAATCCAACTCAAAArCAGCT/GT1/ | Secondary | |
| RH.0BCE12D04779446Z0Z.R | /rhSeq-r/CCACAAAAGCAGCAATACACATATAAArCATCT/GT1/ | Secondary | |
| RH.CF43B917AB504FBZ0Z.R | /rhSeq-r/CGACGAGGATATCCTACGTCrATTTG/GT1/ | Secondary | |
| RH.3C58FDC17E81435Z0Z.R | /rhSeq-r/CGTTTGACTTTACTTCTGTCGAArAGCTT/GT2/ | Secondary | |
| RH.DA4225345CB143AZ0Z.R | /rhSeq-r/TTGCAGGATAATTTAACGTGTTTACACrCTTGT/GT2/ | Secondary |
Troubleshooting
Problem
Absent bands when visualising PCR_2 product on the agarose gel.
Solution
There may be contaminants inhibiting the PCR reaction. In this instance, dilute a small subset of input genomic DNA in IDTE buffer at pH 7.5 or 8.0 (1 in 10) in a DNA Low-bind tube. Run PCR and visualise the PCR_2 product on the agarose gel. If bands are observed, then proceed with a larger sample sets.
Problem
Some of the primers are underperforming in the rebalanced pool.
Solution
If some primers are underperforming using the current calculation (Excel attached in step 2), this might be due to batch-to-batch synthesis variation. Depending on the total reads across samples per marker, try spiking-in those underperforming primers.
Sample Preparation
Input DNA does not require prior clean up or quantification or normalization. If DNA amount is limited (11 μL of DNA is required for this protocol), gDNA can be diluted using IDTE, pH 8.0.
Primer rebalancing
Pool the primers according to the calculations in the attached Excel file for each panel (Panel A and B) and each direction (forward and reverse) separately to prepare rebalanced primer Stock pools.
Pf primer pool_calculation_final.xlsx19.1KB Rebalanced Working Primer Preparation
Thaw an aliquot of the following reagents from -20°C storage.
o Rebalanced rhAmpSeq PCR Panel – Forward Stock Pool (A)
o Rebalanced rhAmpSeq PCR Panel – Reverse Stock Pool (A)
o Rebalanced rhAmpSeq PCR Panel – Forward Stock Pool (B)
o Rebalanced rhAmpSeq PCR Panel – Reverse Stock Pool (B)
After thawing the primers, briefly vortex, then centrifuge.
Prepare working primer pools using a 1 in 5 dilution.
To sequence 96 samples:
o 42μL of A Forward Stock Pool + 168μL of IDTE, pH 7.5
o 42μL of A Reverse Stock Pool + 168μL of IDTE, pH 7.5
o 42μL of B Forward Stock Pool + 168μL of IDTE, pH 7.5
o 42μL of B Reverse Stock Pool+ 168μL of IDTE, pH 7.5
Note
Tip: Prepare multiple aliquots of rhAmpSeq working forward/reverse primer pools and store at -20°C to avoid multiple freeze-thaw cycles.
Perform Targeted rhAmpSeq PCR_1
Thaw the following reagents completely to room temperature(15-20°C).
o 4X rhAmpSeq Library Mix 1
o Rebalanced rhAmpSeq PCR Panel – A Forward Working Pool
o Rebalanced rhAmpSeq PCR Panel – A Reverse Working Pool
o Rebalanced rhAmpSeq PCR Panel – B Forward Working Pool
o Rebalanced rhAmpSeq PCR Panel – B Reverse Working Pool
Note
Important! It is important to perform this step in the morning, as there is no safe stopping point until the end of Step 47
After thawing the reagents, briefly vortex and then centrifuge.
Prepare the PCR_1 master mixes in a Lo-bind Eppendorf tube, separately for the A and B panels, corresponding to the number of samples being processed:
| Component | Per reaction | X 100 (for 96 samples) | |
| 4X rhAmpSeq Library Mix 1 | 5μL | 500μL | |
| 10X rhAmpSeq pf custom PCR Panel – Forward Working Pool | 2μL | 200μL | |
| 10X rhAmpSeq pf custom PCR Panel – Reverse Working Pool | 2μL | 200μL | |
| Total | 9μL | 900μL |
Targeted rhAmpSeq PCR_1 mastermix
Briefly vortex and centrifuge down the mastermix
Prepare two 96-well plates for the A and B panels. Add 9μL of PCR_1 master mix to the designated reaction well for each panel, ensuring the correct master mix is added to the correct plate.
Add 11μL of gDNA to the corresponding wells in both A and B panel plates.
Seal both plates, then briefly vortex and centrifuge.
Place the plates in thermocyclers and run the following program (Lid set to 105°C):
| Step | Cycle | Temperature | Duration | |
| Activate enzyme | 1 | 95°C | 10 min | |
| Amplify | 14 | 95°C | 15 sec | |
| 61°C | 8 min | |||
| Deactivate enzyme | 1 | 99.5°C | 15 min | |
| Hold | 1 | 4°C | Hold |
Targeted rhAmpSeq PCR_1 program
Once the program is complete, remove the plate from the thermocycler and proceed
immediately to Dilute PCR_1 product.
Dilute PCR_1 product
Briefly vortex the PCR_1 product, then centrifuge.
In two new 96-well plates, add 95 μL of Nuclease-Free Water to each well, and label the plates as 1:20 dilution PCR_1 product panel A and panel B.
Transfer 5 μL of the PCR_1 product to each designated well of A and B panel plates (To prepare a final dilution of 1 in 20). Pipette up and down to ensure the entire volume is dispensed.
Seal the plates and thoroughly vortex to mix, then centrifuge before proceeding immediately to Perform Indexing PCR_2.
Perform Indexing PCR_2
Thaw 4X rhAmpSeq Library Mix 2 and xGen 10nt UDI Index Primer Working Plates completely to room temperature (15-20°C).
Note
Important! Stock xGen 10nt UDI Index Primer plates from IDT have Forward and Reverse primers combined at 20 μM total (10 μM each primer). To prepare a working plate (2 μM total), prepare a 1 in 10 dilution with IDTE, pH 7.5 (i.e., 2 μL of Stock Primer + 18 μL of IDTE, pH 7.5).
Briefly vortex, then centrifuge the reagents.
Prepare the PCR_2 master mix in a Lo-bind Eppendorf tube corresponding to the number of samples being processed:
| Component | Per reaction | X 196 ( for 96 samples in panel A and B) | |
| 4X rhAmpSeq Library Mix 2 | 5μL | 980μL | |
| Nuclease Free Water | 2μL | 392μL | |
| Total | 7μL | 1372μL |
Targeted rhAmpSeq PCR_2 mastermix
In two new 96-well plates, add 7 μL of PCR_2 mastermix to each well.
Add 2 μL of xGen 10nt UDI Index Primer Working Concentration to each corresponding
well using a multichannel pipette
Note
Important! Note down the index plate, well position used for each sample and the PCR_1 pf panel name (A or B).
Add 11 μL of diluted rhAmpSeq PCR_1 product to the corresponding well using a multichannel pipette.
Seal the plates, then briefly vortex and centrifuge.
Place the plates in thermocyclers and run the following program (lid set to 105°C):
| Step | Cycle | Temperature | Duration | |
| Activate enzyme | 1 | 95°C | 3 min | |
| Amplify | 24 | 95°C | 15 sec | |
| 60°C | 30 sec | |||
| 72°C | 30 sec | |||
| Final extension | 1 | 72°C | 1 min | |
| Hold | 1 | 4°C | Hold |
Targeted rhAmpSeq PCR_2 program
Once the program is complete, remove the plates from the thermocyclers and proceed immediately to Pool libraries.
Optional: PCR success can be confirmed by gel electrophoresis on 2% agarose gel after reaching the nearest safe stopping point.
Pool libraries
Using a multichannel pipette, pool each row from designated A and B panel plates by transferring 5 μL of each indexed library into one 8-well strip tube (use 10 μL if the total number of individual libraries processed is less than 20 samples).
Note
Tip: Minimize sample-to-sample variability with precise pipetting.
Cap the strip tube, briefly vortex, then centrifuge down.
Combine all libraries from the strip tube into a single 1.5 or 2 mL LoBind tube.
Note
Important! Pool the complete volume from each well for an even sample coverage.
Properly seal and store the plates with remaining individual indexed libraries at -20°C then proceed immediately to clean up the pooled libraries.
Clean up library
Transfer 100 μLof the rhAmpSeq library pool to a new 1.5 mL tube.
Vortex the SPRI beads thoroughly before use.
Add 70 μL of SPRI (0.7X) to the library pool.
Thoroughly mix the contents of the tube by pipetting up and down.
Incubate for 10 minutes at room temperature.
Prepare 2 mL of fresh 80% ethanol solution by combining 400 μL of molecular-grade water and 1,600 μL of molecular-grade ethanol (Absolute ethanol).
Briefly pulse spin down the tube then place it on a magnetic rack for 5 minutes, or until the solution is clear.
Keeping the tube on the magnet, do the following:
Aspirate with the pipette, then discard the supernatant.
Add 1000 μL of 80% ethanol to the tube.
Incubate at room temperature for 30 seconds.
Aspirate, then discard the supernatant.
Repeat the 80% ethanol wash one more time (steps 40.2 - 40.4).
Using a new P200 pipette tip, remove the remaining ethanol from the tube.
Allow the beads to dry for 3 minutes at room temperature.
Remove the tube from the magnet.
Add 22 μL of IDTE, pH 8.0, to elute the library pool.
Thoroughly vortex to fully resuspend the beads, then briefly pulse spin down the tube.
Incubate at room temperature for 3 minutes.
Place the tube on the magnet to collect the beads for 1 minute, or until the solution is clear.
While keeping the tube on the magnet, transfer 20 μL of the final library pool elution into a new 1.5 mL LoBind tube, ensuring no beads are carried over.
Proceed to quantify and check the size of the library.
Safe stopping point. Store any remaining library pool at -20°C for up to 3 weeks. using the stored library make sure to repeat the library QC steps.
Library QC
Quantify the library concentration using Illumina NGS library quantification kit (such as The Invitrogen Collibri Library Quantification Kit).
Using capillary electrophoresis, check the fragment size of the library before and after beads clean-up to ensure that adapter dimers have been successfully removed.
Sequencing
Follow Illumina's recommended protocol for a 2 x 150bp paired-end sequencing run on your Illumina platform.
Protocol references
1. Kleinecke, M., Sutanto, E., Rumaseb, A. et al. Microhaplotype deep sequencing assays to capture Plasmodium vivax infection lineages. Nat Commun 16, 7192 (2025). https://doi.org/10.1038/s41467-025-62357-x
2. Jacob, C. G., Nguyen, T.-N., Mayxay, M., et al. (2021). Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination. eLife, 10, Article e62997. https://doi.org/10.7554/eLife.62997
3. Aranda-Díaz, A., Neubauer Vickers, E., Murie, K. et al. Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health. Sci Rep 15, 10737 (2025). https://doi.org/10.1038/s41598-025-94716-5
Acknowledgements
We thank the patients who contributed their samples to the study, and the health workers and field teams who assisted with sample collection for use in establishing this assay.