Supplementary Table 1 Continued

Supplementary Table 1 Table of whole-genome sequencing data of the dwarf pony and 26 equid reference samples. The experiment number, breed type, mapping metrics and number of variants are shown. Experiments Breed Platform Average read Reads mapped Bases mapped Mean Number of Number of (SRA) length coverage (X) SNPs INDELs SRX1976860 Miniature NextSeq 500 143 290180317 41683264273 17.61 7068170 923406 Horse SRX384479 Dülmen Horse Illumina 99 383618813 38301826028 16.18 7144970 1023448 HiSeq 2000 SRX389472 Arabian Illumina 99 367202161 36662432668 15.49 6969138 999510 HiSeq 2000 SRX290477, Arabian Illumina 98 1012025750 84914966541 35.87 6463296 865749 SRX290478, HiSeq 2000 SRX297080, SRX297081, SRX297085, SRX297086 SRX389475 Sorraia Illumina 99 335336672 33467221874 14.14 6872814 990355 HiSeq 2000 SRX1131820 Sorraia Illumina 240 142841759 34295369714 14.49 6990495 1070836 MiSeq SRX389480 Hanoverian Illumina 99 679791424 67885114371 28.68 6985502 1011746 HiSeq 2000 SRX389477 Hanoverian Illumina 99 295736070 29533047810 12.48 6865130 982519 HiSeq 2000 Supplementary Table 1 continued. Experiments Breed Platform Average read Reads mapped Bases mapped Mean Number of Number of (SRA) length coverage (X) SNPs INDELs SRX1131705 Hanoverian Illumina 100 293335169 29587965748 12.50 6847094 971512 HiSeq 2000 SRX1131785 Hanoverian Illumina 100 309152704 31183340026 13.17 6823107 970630 HiSeq 2000 SRX1131818 Saxon- Illumina 243 161045282 39166365318 16.55 7300614 1092034 Thuringian MiSeq Heavy Warmblood SRX396629 Thoroughbred Illumina 99 425474117 42504539882 17.96 3970983 772187 HiSeq 2000 SRX290677, Donkey Illumina 67 683656952 46311142906 19.56 28353882 2529142 SRX290675, HiSeq SRX290673 2000 SRX297956, Norwegian Illumina 98 864622165 46311142908 19.56 6652284 803042 SRX297960, Fjord HiSeq SRX298219, 2000 SRX298220, SRX298223 SRX298240, Standardbred Illumina 98 1039666520 102668352861 43.37 6899658 927888 SRX298241, HiSeq SRX298242, 2000 SRX298268, SRX299496, SRX299497, SRX299498

Supplementary Table 1 continued. Experiments Breed Platform Average read Reads mapped Bases mapped Mean Number of Number of (SRA) length coverage (X) SNPs INDELs SRX302108, Icelandic Illumina 98 1553268915 153080940423 64.67 952145 7218698 SRX302107, HiSeq SRX302106, 2000 SRX302105, SRX302104, SRX302103, SRX299500, SRX299499 SRX305128, Przewalski Illumina 98 973017124 95822928305 40.48 7660788 975616 SRX305127, HiSeq SRX302128, 2000 SRX302113, SRX302111, SRX302110, SRX302101, SRX302100, SRX302099, SRX302098 SRX535352 Marwari Illumina 99 1007489535 100590435123 42.50 7118554 1044639 HiSeq 2000 SRX850674 Connemara Illumina 100 160096734 16069448775 6.79 6798146 944679 pony HiSeq 2000 SRX850675 Connemara Illumina 100 154110447 15468310770 6.54 6629842 931950 pony HiSeq 2000 ERX947604 Shetland Pony Illumina 100 583432122 58817988824 24.85 6834797 943714 HiSeq 2000 Supplementary Table 1 continued. Experiments Breed Platform Average read Reads mapped Bases mapped Mean Number of Number of (SRA) length coverage (X) SNPs INDELs ERX947605 Shetland Pony Illumina 100 640150066 64530347071 27.26 7133425 972944 HiSeq 2000 SRX305128 Przewalski Illumina 98 163194844 16124324742 6.81 3525323 373386 HiSeq 2000 SRX305127 Przewalski Illumina 98 262151268 25910617034 10.95 5428472 568671 HiSeq 2000 SRX302128 Przewalski Illumina 97 225848396 22110919669 9.34 6219957 668235 HiSeq 2000 SRX302111 Przewalski Illumina 98 207292884 20341365916 8.59 5584455 583030 HiSeq 2000 SRX302110 Przewalski Illumina 98 99152994 9803579023 4.14 3912846 380057 HiSeq 2000