| Species | Sequencing platform | Batch | Sample ID |
| Apodemus sylvaticus | NextSeq single + paired; Miseq | 1 | SMG3823 |
| Apomys lubangensis | NextSeq single + paired; Miseq | 1 | JAE169_PHL |
| Archboldomys luzonensis | NextSeq single + paired; Miseq | 1 | EAR1826_PHL |
| Berylmys bowersi | NextSeq single + paired; Miseq | 1 | ABTC116431 |
| Bulimus bagobus | NextSeq single + paired; Miseq | 1 | JAE1712 |
| Bullimus salomonseni | NextSeq single + paired; Miseq | 1 | JAE3320 |
| Bunomys chrysocomus | NextSeq single + paired; Miseq | 1 | JAE4867 |
| Chiropodomys gliroides | NextSeq single + paired; Miseq | 1 | Z25153 |
| Chrotomys mindorensis | NextSeq single + paired; Miseq | 1 | JAE520_PHL |
| Colomys goslingi | NextSeq single + paired; Miseq | 1 | TCD4175 |
| Crunomys celebensis | NextSeq single + paired; Miseq | 1 | Z21894 |
| Echiothrix centrosa | NextSeq single + paired; Miseq | 1 | Z27993_SUL |
| Gracilimus radix | NextSeq single + paired; Miseq | 1 | Z08508_SUL |
| Grammomys dryas | NextSeq single + paired; Miseq | 1 | LSUMZ37717 |
| Haeromys minahassae | NextSeq single + paired; Miseq | 1 | JAE4996 |
| Hybomys univittatus | NextSeq single + paired; Miseq | 1 | TCD4026 |
| Hydromys chrysogaster | NextSeq single + paired; Miseq | 1 | Z5248_SAHUL |
| Hylomyscus vulcanorum | NextSeq single + paired; Miseq | 1 | TCD4382 |
| Hyorhinomys stuempkei | NextSeq single + paired; Miseq | 1 | JAE4661_SUL |
| Lemniscomys striatus | NextSeq single + paired; Miseq | 1 | TCD4711 |
| Leopoldomys sabanus | NextSeq single + paired; Miseq | 1 | Z25191 |
| Lorentzimys nouhuysi | NextSeq single + paired; Miseq | 1 | ABTC46314_SAHUL |
| Malacomys longipes | NextSeq single + paired; Miseq | 1 | TCD4253 |
| Margaretamys parvus | NextSeq single + paired; Miseq; Hiseq4000 | 1 | NMV Z21833 |
| Mastacomys fuscus | NextSeq single + paired; Miseq | 1 | ABTC07354_SAHUL |
| Maxomys surifer | NextSeq single + paired; Miseq | 1 | JAE3632 |
| Melasmothrix naso | NextSeq single + paired; Miseq | 1 | Z21808_SUL |
| Melomys rufescens | NextSeq single + paired; Miseq | 1 | ABTC44798_SAHUL |
| Niviventer lepturus | NextSeq single + paired; Miseq | 1 | JAE4746 |
| Paruromys dominator | NextSeq single + paired; Miseq | 1 | JAE4870 |
| Paucidentomys vermidax | NextSeq single + paired; Miseq | 1 | Z21914_SUL |
| Phloeomys pallidus | NextSeq single + paired; Miseq | 1 | JEC43 |
| Praomys degraaffi | NextSeq single + paired; Miseq | 1 | TCD4312 |
| Rhynchomys isarogensis | NextSeq single + paired; Miseq | 1 | JAE2195_PHL |
| Sommeromys macrorhinos | NextSeq single + paired; Miseq | 1 | Z21740_SUL |
| Sundamys muelleri | NextSeq single + paired; Miseq | 1 | JAE1283 |
| Taeromys punicans | NextSeq single + paired; Miseq; Hiseq4000 | 1 | MVZ225815 |
| Tateomys macrocercus | NextSeq single + paired; Miseq | 1 | NMVZ21834 |
| Tateomys rhinogradoides | NextSeq single + paired; Miseq | 1 | Z21785_SUL |
| Waiomys mamasae | NextSeq single + paired; Miseq | 1 | Z20624_SUL |
| Bunomys andrewsi | Hiseq; Hiseq2500 | 2 | NMVZ21879 |
| Maxomys musschenbroekii | Hiseq; Hiseq2500 | 2 | NMVZ21924 |
| Rattus exulans | Hiseq; Hiseq2500 | 2 | JLP25332 |
| Rattus hoffmanni | Hiseq; Hiseq2500; Hiseq4000 | 2 | LSUMZ39187 |
| Rattus leucopus | Hiseq; Hiseq2500 | 2 | QM19102 |
| Rattus lutreolus | Hiseq; Hiseq2500 | 2 | SCUC132 |
| South Australian Museum" Rattus | Indonesia; New Guinea | Hiseq; Hiseq2500 | |
| Rattus villosissimus | Hiseq; Hiseq2500 | 2 | NMVC36845 |
| Mus caroli | Hiseq2000 | 3 | EME2873 |
| Mus cervicolor | Hiseq2000 | 3 | PKT631 |
| Mus cookii | Hiseq2000 | 3 | EME2882 |
| Mus macedonicus | Hiseq2000 | 3 | RDS10150 |
| Mus minutoides | Hiseq2000 | 3 | EME2791 |
| Mus molossinus | Hiseq2000 | 3 | |
| Mus musculus castaneus | Hiseq2000 | 3 | |
| Mus musculus domesticus | Hiseq2000 | 3 | LEWES |
| Mus musculus musculus | Hiseq2000 | 3 | CZII |
| Mus musculus reference | Hiseq2000 | 3 | |
| Mus pahari | Hiseq2000 | 3 | PKT627 |
| Mus platythrix | Hiseq2000 | 3 | EME2769 |
| Mus spicilegus | Hiseq2000 | 3 | EME2745 |
| Mus spretus | Hiseq2000 | 3 | EME2521 |
| Abeomelomys sevia | Hiseq4000 | 4 | KUM 161018 |
| Aethomys hindei | Hiseq4000 | 4 | MVZ196257 |
| Aethomys nyikae | Hiseq4000 | 4 | FMNH196708 |
| Anisomys imitator | Hiseq4000 | 4 | ABTC 45107 |
| Bandicota indica | Hiseq4000 | 4 | ABTC 119185 |
| Batomys russatus | Hiseq4000 | 4 | KU165776 |
| Berylmys mackenzii | Hiseq4000 | 4 | ABTC 116402 |
| Carpomys melanurus | Hiseq4000 | 4 | FMNH198723 |
| Chiromyscus chiropus | Hiseq4000 | 4 | ABTC 69097 |
| Chiruromys vates | Hiseq4000 | 4 | ABTC 43096 |
| Chrotomys whiteheadi | Hiseq4000 | 4 | KU168311 |
| Coccymys ruemmleri | Hiseq4000 | 4 | ABTC 49489 |
| Crateromys heaneyi | Hiseq4000 | 4 | KU165014 |
| Crunomys melanius | Hiseq4000 | 4 | KU168403 |
| Crunomys melanius | Hiseq4000 | 4 | KU168558 |
| Dasymys incomtus | Hiseq4000 | 4 | LSUMZ37702 |
| Dasymys montanus | Hiseq4000 | 4 | FMNH144389 |
| Genus sp nov | Hiseq4000 | 4 | NMV Z21816 |
| Grammomys dryas | Hiseq4000 | 4 | LSUMZ37716 |
| Halmaheramys bokimekot | Hiseq4000 | 4 | 33262 (WD225) |
| Hybomys lunaris | Hiseq4000 | 4 | LSUMZ37734 |
| Hybomys planifrons | Hiseq4000 | 4 | R24117 |
| Hydromys sp nov | Hiseq4000 | 4 | YS391 |
| Hylomyscus stella | Hiseq4000 | 4 | LSUMZ37742 |
| Kadarsanomys sodyi | Hiseq4000 | 4 | MZB-Sample |
| Lenomys meyeri | Hiseq4000 | 4 | LSUMZ39079 |
| Leptomys elegans | Hiseq4000 | 4 | ABTC 45741 |
| Limnomys sibuanus | Hiseq4000 | 4 | FMNH147948 |
| Macruromys major | Hiseq4000 | 4 | ABTC 43909 |
| Mallomys rothschildi | Hiseq4000 | 4 | ABTC 47402 |
| Mammelomys lanosus | Hiseq4000 | 4 | ABTC 47208 |
| Margaretamys christinae | Hiseq4000 | 4 | T_Mar1 |
| Microhydromys richardsoni | Hiseq4000 | 4 | ANWC M35851 |
| Mirzamys louiseae | Hiseq4000 | 4 | ABTC 133754 |
| Mus musculoides | Hiseq4000 | 4 | LSUMZ37820 |
| Musseromys anacuao | Hiseq4000 | 4 | FMNH209523 |
| Nesokia indica | Hiseq4000 | 4 | ABTC 117074 |
| Niviventer bukit | Hiseq4000 | 4 | LSUMZ38136 |
| Niviventer cremoriventer | Hiseq4000 | 4 | LSUMZ38141 |
| Niviventer rapit | Hiseq4000 | 4 | LSUMZ38196 |
| Oenomys hypoxanthus | Hiseq4000 | 4 | LSUMZ37838 |
| Otomys denti | Hiseq4000 | 4 | LSUMZ37840 |
| Otomys tropicalis | Hiseq4000 | 4 | LSUMZ37841 |
| Papagomys armandvillei | Hiseq4000 | 4 | WAM M32592 |
| Parahydromys asper | Hiseq4000 | 4 | ABTC 45798 |
| Paraleptomys wilhelmina | Hiseq4000 | 4 | H126 = ABTC133716 |
| Pelomys isseli | Hiseq4000 | 4 | FMNH137886 |
| Pelomys minor | Hiseq4000 | 4 | FMNH219213 |
| Phloeomys cumingi | Hiseq4000 | 4 | FMNH198472 |
| Pithecheir melanurus | Hiseq4000 | 4 | LSUMZ38198 |
| Pogonomelomys mayeri | Hiseq4000 | 4 | AM.M.21849 |
| Pogonomys macrourus | Hiseq4000 | 4 | ABTC 43144 |
| Praomys jacksoni | Hiseq4000 | 4 | TCD4655 |
| Pseudohydromys pumehanae | Hiseq4000 | 4 | ABTC 43920 |
| Rattus argentiventer | Hiseq4000 | 4 | LSUMZ38199 |
| Rattus xanthurus | Hiseq4000 | 4 | LSUMZ39196 |
| Saxatilomys paulinae | Hiseq4000 | 4 | ABTC 116266 |
| Solomys salebrosus | Hiseq4000 | 4 | ABTC 64864 |
| Sundamys annandalei | Hiseq4000 | 4 | YS118 |
| Taeromys callitrichus | Hiseq4000 | 4 | LSUMZ37153 |
| Taeromys taerae | Hiseq4000 | 4 | LSUMZ39224 |
| Tarsomys apoensis | Hiseq4000 | 4 | KU167148 |
| Thamnomys kempi | Hiseq4000 | 4 | TCD4437 |
| Thamnomys venustus | Hiseq4000 | 4 | LSUMZ37935 |
| Uromys caudimaculatus | Hiseq4000 | 4 | DT10 Uc01 |
| Uromys sp nov | Hiseq4000 | 4 | YS380 |
| Vandeleuria oleracea | Hiseq4000 | 4 | ABTC 116404 |
| Xenuromys barbatus | Hiseq4000 | 4 | Y250 = ABTC 129204 |
| Xeromys myoides | Hiseq4000 | 4 | ABTC 30709 |
| Zelotomys woosnami | Hiseq4000 | 4 | TTU-M115260 |
| Conilurus albipes | Hiseq2500 | 5 | NMV-c7585 |
| Conilurus penicillatus | Hiseq2500 | 5 | M14056 |
| Leggadina forresti | Hiseq2500 | 5 | WAMM62323 |
| Leggadina lakedownensis | Hiseq2500 | 5 | WAMM21623 |
| Leporillus apicalis | Hiseq2500 | 5 | C90 |
| Leporillus conditor | Hiseq2500 | 5 | ABTC13335 |
| Mastacomys fuscus | Hiseq2500 | 5 | M13957 |
| Mastacomys fuscus | Hiseq2500 | 5 | NMB C37546 |
| Mesembriomys gouldii | Hiseq2500 | 5 | ABTC7449 |
| Mesembriomys macrurus | Hiseq2500 | 5 | ABTC7337 |
| Notomys alexis | Hiseq2500 | 5 | U1308 |
| Notomys alexis | Hiseq2500 | 5 | ABTC94521 |
| Notomys amplus | Hiseq2500 | 5 | NMV-C512 |
| Notomys aquilo | Hiseq2500 | 5 | M-32455 |
| Notomys cervinus | Hiseq2500 | 5 | M22857 |
| Notomys fuscus | Hiseq2500 | 5 | M22830 |
| Notomys longicaudatus | Hiseq2500 | 5 | C6278 |
| Notomys macrotis | Hiseq2500 | 5 | ZD-1841-1167 |
| Notomys mitchellii | Hiseq2500 | 5 | M21518 |
| Pseudomys albocinereus | Hiseq2500 | 5 | WAMM18855 |
| Pseudomys apodemoides | Hiseq2500 | 5 | M16672 |
| Pseudomys auritus | Hiseq2500 | 5 | 1846_4_4_67 |
| Pseudomys australis | Hiseq2500 | 5 | M25541 |
| Pseudomys bolami | Hiseq2500 | 5 | ABTC08077 |
| Pseudomys bolami | Hiseq2500 | 5 | ABTC107389 |
| Pseudomys calabyi | Hiseq2500 | 5 | U4324 |
| Pseudomys chapmani | Hiseq2500 | 5 | WAMM29440 |
| Pseudomys delicatulus | Hiseq2500 | 5 | JM18363 |
| Pseudomys delicatulus | Hiseq2500 | 5 | M29247 |
| Pseudomys delicatulus | Hiseq2500 | 5 | U1509 |
| Pseudomys delicatulus | Hiseq2500 | 5 | WAMM29247 |
| Pseudomys desertor | Hiseq2500 | 5 | ABTC41464 |
| Pseudomys fieldi | Hiseq2500 | 5 | ABTC08164 |
| Pseudomys fumeus | Hiseq2500 | 5 | ABTC08168 |
| Pseudomys gouldii | Hiseq2500 | 5 | C955 |
| Pseudomys gracilicaudatus | Hiseq2500 | 5 | ABTC08163 |
| Pseudomys hermannsburgensis | Hiseq2500 | 5 | ABTC08067 |
| Pseudomys hermmannsburgensis | Hiseq2500 | 5 | M7890 |
| Pseudomys higginsi | Hiseq2500 | 5 | UC1421 |
| Pseudomys johnsoni | Hiseq2500 | 5 | WAMM56280 |
| Pseudomys johnsoni | Hiseq2500 | 5 | ABTC08053 |
| Pseudomys nanus | Hiseq2500 | 5 | U1448 |
| Pseudomys novaehollandiae | Hiseq2500 | 5 | ABTC08140 |
| Pseudomys novaehollandiae | Hiseq2500 | 5 | NMV_C22127 |
| Pseudomys occidentalis | Hiseq2500 | 5 | ABTC08043 |
| Pseudomys oralis | Hiseq2500 | 5 | RAT7 |
| Pseudomys patrius | Hiseq2500 | 5 | JM10865 |
| Pseudomys pilligaensis | Hiseq2500 | 5 | ABTC18120 |
| Pseudomys shortridgei | Hiseq2500 | 5 | M62127 |
| Pseudomys shortridgei | Hiseq2500 | 5 | Z25113 |
| Rattus colletti | Hiseq2500 | 5 | RAT25 |
| Rattus tunneyi | Hiseq2500 | 5 | RAT130 |
| Zyzomys argurus | Hiseq2500 | 5 | ABTC61630 |
| Zyzomys maini | Hiseq2500 | 5 | ABTC07900 |
| Zyzomys palatalis | Hiseq2500 | 5 | ABTC30744 |
| Zyzomys pedunculatus | Hiseq2500 | 5 | Z34925 |
| Zyzomys woodwardi | Hiseq2500 | 5 | WAMM21724 |
| Anonymomys mindorensis | Hiseq4000 | 6 | FMNH2222010 |
| Arvicanthus neumanni | Hiseq4000 | 6 | FMNH158037 |
| Arvicanthus niloticus | Hiseq4000 | 6 | MNHN1999201 |
| Bunomys torajae | Hiseq4000 | 6 | NMV_Z21736 |
| Crossomys moncktoni | Hiseq4000 | 6 | ABTC 46614 |
| Dephomys defua | Hiseq4000 | 6 | MNHNR24062 |
| Eropeplus canus | Hiseq4000 | 6 | NMV Z21733 |
| Heimyscus fumosus | Hiseq4000 | 6 | FMNH167810 |
| Hyomys goliath | Hiseq4000 | 6 | ABTC42697 |
| Lophiomys imhausi | Hiseq4000 | 6 | UM5152 |
| Lophuromys woosnami | Hiseq4000 | 6 | LSUMZ37793 |
| Mastomys natalensis | Hiseq4000 | 6 | TCD4162 |
| Micaelemys namaquensis | Hiseq4000 | 6 | MNHN1987009 |
| Mylomys dybowskii | Hiseq4000 | 6 | MNHN1997072 |
| Myomyscus verreauxii | Hiseq4000 | 6 | MNHN1999102 |
| Rattus morotaiensis | Hiseq4000 | 6 | ASA M29 |
| Rhabdomys pumilio | Hiseq4000 | 6 | MNHN1995065 |
| Stochomys longicaudatus | Hiseq4000 | 6 | MNHN1999459 |
| Taeromys celebensis | Hiseq4000 | 6 | NMV_Z20637 |
| Taeromys hamatus | Hiseq4000 | 6 | NMV_Z63317 |
| Thallomys paedulcus | Hiseq4000 | 6 | FMNH158089 |
