###################################################### ### This README file contains a list of the files ### ### and descriptions for each file in this Dryad ### ### repository. NOTE: The md5sum is also given for ### ### each file. You can verify that you do not ### ### have a corrupted file by matching the md5sum ### ### for each file given below with the output of ### ### UNIX terminal commands like "md5 file" or ### ### "md5sum file". The various file formats are ### ### described in appendix 1 at the bottom. The ### ### computer code and commands used to generate ### ### the results are available at my GitHub page: ### ### https://github.com/rfitak/Mexican_Wolf_SNPs ### ### Thanks for promoting data-sharing!!! ### ### Bob Fitak 2/7/2018 ### ###################################################### # Note # As mentioned in the manuscript the Mexican wolf sample information is available in Supplementary Table S1. Computer code and scripts for processing the data are available at GitHub - (https://github.com/rfitak/Mexican_Wolf_SNPs). The raw data from all other canid (wolf and dog) genotypes used for comparison can be found at: - Medrano et al. 2014; Cronin et al. 2015a Dryad doi: http://dx.doi.org/10.5061/dryad.284tf - Stronen et al. 2015a; b Dryad doi: http://dx.doi.org/10.5061/dryad.p6598 - Vernau et al. 2013 Please contact the corresponding author. - Vaysse et al. 2011 http://dogs.genouest.org/SWEEP.dir/Supplemental.html The MERGED dataset below does contain these data in order to repeat all analyses from this study. #################################################### ###################### Files ####################### #################################################### FILE: MW_raw_data.tar.gz MD5SUM: d81920fdd1adbc73cee72301340b7652 DESCRIPTION: This file, once unpacked, contains the raw data from the CanineHD beadchip genotyping. There are eight subfolders, each representing one chip and 12 samples (96 total samples). The files within each folder are proprietary formats for use with Illumina's GenomeStudio software for conversion into actual genotypes. These files are useful for those who which to perform additional quality-control assessments of the fluorescence values and genotype scores. Again, these files can only be interpreted by the GenomeStudio software available from Illumina. Additionally, the two clustering files used to call genotypes are also provided. The MD5 tags for all files are listed below: FORMAT: tar.gz File: CanineHD_A.egt md5: fa82c03154f1463d96e1713682e61660 Description: This file contains the clustering data used to call genoptyes from the raw CanineHD BeadChip data. Used in Illumna's GenomeStudio software. File: CanineHD_A.bpm md5: 287fdd32820c5253bea04a5cc7a07b1d Description: This file contains the SNP metadata used to identify each SNP and compare it back to the reference genome. Used in Illumna's GenomeStudio software. Folder: 5511344025 File: 5511344025_R01C01.gtc md5: aabc8cb29dad2e138cc1e5d6588412b1 File: 5511344025_R01C01.gtc.txt md5: 99d660603781948e510549ebd563590e File: 5511344025_R01C01_Grn.idat md5: 2d22d01e266396a59a97b0e17ad27934 File: 5511344025_R01C01_Red.idat md5: 05888b4cb93e035216c41541e9d44630 File: 5511344025_R01C02.gtc md5: 4563c0a9a8dc5552f6d735b186f580c8 File: 5511344025_R01C02.gtc.txt md5: 99d660603781948e510549ebd563590e File: 5511344025_R01C02_Grn.idat md5: 12046941c7f686d19b1cf30d702087bd File: 5511344025_R01C02_Red.idat md5: 7ead5a0345b1d2ea1b5c6ed7255dbc64 File: 5511344025_R02C01.gtc md5: 5b73287a87be8bd6f6f87f223fd29a2b File: 5511344025_R02C01.gtc.txt md5: 328f8292139a701b120d437ace61b8d8 File: 5511344025_R02C01_Grn.idat md5: ef95d50e92e9c9a9055fd04e6037d452 File: 5511344025_R02C01_Red.idat md5: 5ea485bcf9b0b037c3d99d2180b567d4 File: 5511344025_R02C02.gtc md5: 233907e18eeac7463590c29b4833e903 File: 5511344025_R02C02.gtc.txt md5: 99d660603781948e510549ebd563590e File: 5511344025_R02C02_Grn.idat md5: 60484f37d0bf88a804270260fa6baaab File: 5511344025_R02C02_Red.idat md5: 341aaa133ea385af7f0916f9eadb66f1 File: 5511344025_R03C01.gtc md5: 2e7a43ab0215fc1a09d0c6e2dc6aeed8 File: 5511344025_R03C01.gtc.txt md5: 5b5da506f584a7fe8de2ac597d674c91 File: 5511344025_R03C01_Grn.idat md5: 162150a8c0d2694c26384d395e9ebd00 File: 5511344025_R03C01_Red.idat md5: f77ad54832ac82a9a37d9437f5d5e79c File: 5511344025_R03C02.gtc md5: ed2c23cc8fe1de42f3343a823f342a55 File: 5511344025_R03C02.gtc.txt md5: 328f8292139a701b120d437ace61b8d8 File: 5511344025_R03C02_Grn.idat md5: 58cf8d829102134aa664557a25fd70f5 File: 5511344025_R03C02_Red.idat md5: 7e99a8d30cd012cc07f036678116460a File: 5511344025_R04C01.gtc md5: 06ecd0b03b02628a9efaec1a573b6394 File: 5511344025_R04C01.gtc.txt md5: 99d660603781948e510549ebd563590e File: 5511344025_R04C01_Grn.idat md5: e48b4a62d993202db9486a379e0311bc File: 5511344025_R04C01_Red.idat md5: 24427fe0dd20ecb7e8fd5fda871df561 File: 5511344025_R04C02.gtc md5: 6700bb5e5634d08c4e2077908906caa4 File: 5511344025_R04C02.gtc.txt md5: 328f8292139a701b120d437ace61b8d8 File: 5511344025_R04C02_Grn.idat md5: 90b64768d89cc83b6a0213ce1f0c9c57 File: 5511344025_R04C02_Red.idat md5: 301cbac5b52601bd006deecbdab2d41e File: 5511344025_R05C01.gtc md5: 579064b1c778410c7165571e280bf155 File: 5511344025_R05C01.gtc.txt md5: 5b5da506f584a7fe8de2ac597d674c91 File: 5511344025_R05C01_Grn.idat md5: 5582d514a7670a9e1a49dd5ec8e19c8f File: 5511344025_R05C01_Red.idat md5: bf1971cbea31797a19ff4363b4490430 File: 5511344025_R05C02.gtc md5: 5838865fff0ceeec81db76d968c47a5d File: 5511344025_R05C02.gtc.txt md5: 99d660603781948e510549ebd563590e File: 5511344025_R05C02_Grn.idat md5: 41715942b6f5e73b9c553ab3116c74af File: 5511344025_R05C02_Red.idat md5: 204e37b6b93228b8e042b9c58c87d9ee File: 5511344025_R06C01.gtc md5: 21cb74ed5d93b1ba0aea86024f0121da File: 5511344025_R06C01.gtc.txt md5: dc0dae53e4f7d7013a4518a5d535de23 File: 5511344025_R06C01_Grn.idat md5: 47a2b0628513569af2913a30105485ad File: 5511344025_R06C01_Red.idat md5: bfa52ff4eded09da9d7f9300796d100b File: 5511344025_R06C02.gtc md5: fed1184a791df9aad53769e9717aefec File: 5511344025_R06C02.gtc.txt md5: 5b5da506f584a7fe8de2ac597d674c91 File: 5511344025_R06C02_Grn.idat md5: 394a3c24d131bb3aea77afcd72995042 File: 5511344025_R06C02_Red.idat md5: 7abcbc432d46ababd27439d5c1c4d9f3 Folder: 5511344026 File: 5511344026_R01C01.gtc md5: 085476579f95a982e99ad81346dfa924 File: 5511344026_R01C01.gtc.txt md5: dc0dae53e4f7d7013a4518a5d535de23 File: 5511344026_R01C01_Grn.idat md5: f9cf570616f6c6dff7edd50065c641d0 File: 5511344026_R01C01_Red.idat md5: cc565c93495c681767515a3df0df2a3a File: 5511344026_R01C02.gtc md5: 6e86fe358d916cc4d474f9a04ebb3509 File: 5511344026_R01C02.gtc.txt md5: dc0dae53e4f7d7013a4518a5d535de23 File: 5511344026_R01C02_Grn.idat md5: 5a505d350f03232e643a60434714cda2 File: 5511344026_R01C02_Red.idat md5: 3fb35bed6b8436ae85e35577087dccca File: 5511344026_R02C01.gtc md5: 7cc65f2814a6f4c28596b3b1c99bf47c File: 5511344026_R02C01.gtc.txt md5: 05691610a5766d8672876f2d2be04255 File: 5511344026_R02C01_Grn.idat md5: e0763b9cedfcb772bedff68ae1f42f82 File: 5511344026_R02C01_Red.idat md5: 69fc898833f1c06754577cf3f77b114d File: 5511344026_R02C02.gtc md5: 42776f64827996ba3462be1020f6d288 File: 5511344026_R02C02.gtc.txt md5: 328f8292139a701b120d437ace61b8d8 File: 5511344026_R02C02_Grn.idat md5: a82d3550a0e45ea950e035f9bb8e6599 File: 5511344026_R02C02_Red.idat md5: 0ab75dd894b71d42403beaa2609a5ff9 File: 5511344026_R03C01.gtc md5: 54ba4a0dc15a212492fdf1bfb857a123 File: 5511344026_R03C01.gtc.txt md5: 05691610a5766d8672876f2d2be04255 File: 5511344026_R03C01_Grn.idat md5: 1c8647ee2b42498aaf46105b0f51eafd File: 5511344026_R03C01_Red.idat md5: c9b332b9a9a23904ca42bef8d343de89 File: 5511344026_R03C02.gtc md5: 238ed94013538e71cd0dd8b8f6a4c42d File: 5511344026_R03C02.gtc.txt md5: 1d858a240c47a63950e3fc2c3ada8c84 File: 5511344026_R03C02_Grn.idat md5: 1af88adaf0bf21268b7ce72dc13c5619 File: 5511344026_R03C02_Red.idat md5: 46176a7ba7dc1ee5f79239a2d7601bd5 File: 5511344026_R04C01.gtc md5: e9f5d4853274b910fc97a38d2b2a1cf7 File: 5511344026_R04C01.gtc.txt md5: 05691610a5766d8672876f2d2be04255 File: 5511344026_R04C01_Grn.idat md5: 37afd52145efd34f454be6da5e7748c9 File: 5511344026_R04C01_Red.idat md5: 69334c39fa8c9920c834597a0b055772 File: 5511344026_R04C02.gtc md5: c2b570e58b46b6d4520bea8cde268fa0 File: 5511344026_R04C02.gtc.txt md5: 05691610a5766d8672876f2d2be04255 File: 5511344026_R04C02_Grn.idat md5: cb9f0e87c11622326396ce416c902f28 File: 5511344026_R04C02_Red.idat md5: 2a16200673be1224e4031e9075fdf170 File: 5511344026_R05C01.gtc md5: 119823ce5ed983652f13cc3b984e2c67 File: 5511344026_R05C01.gtc.txt md5: dc0dae53e4f7d7013a4518a5d535de23 File: 5511344026_R05C01_Grn.idat md5: 3bd1ba23ca721b309726f2b35e6a1ff9 File: 5511344026_R05C01_Red.idat md5: 7f3d3f967f9f5037c98228290fc8e892 File: 5511344026_R05C02.gtc md5: a9cf3bc998848695c94bf794fc4f814b File: 5511344026_R05C02.gtc.txt md5: 05691610a5766d8672876f2d2be04255 File: 5511344026_R05C02_Grn.idat md5: 447bc1afb921a6af147d623449e19624 File: 5511344026_R05C02_Red.idat md5: 603520dad60a34260476b44fca7ebe78 File: 5511344026_R06C01.gtc md5: 526c34ce5b2c677171b321122d5b2581 File: 5511344026_R06C01.gtc.txt md5: 73d0b45e6a22a16cf48e55c1d282889c File: 5511344026_R06C01_Grn.idat md5: 535ccf61720d756fb2fdc37706f8ed34 File: 5511344026_R06C01_Red.idat md5: 04e14e601ca4a96cdfd8179fb4d0a3a1 File: 5511344026_R06C02.gtc md5: 6d56209bdb636846a00c54bb07561b28 File: 5511344026_R06C02.gtc.txt md5: 05691610a5766d8672876f2d2be04255 File: 5511344026_R06C02_Grn.idat md5: f89a1013dfc316f717ec537a575a1e72 File: 5511344026_R06C02_Red.idat md5: e7353785e2467d1eb96d281c4029c412 Folder: 5511344027 File: 5511344027_R01C01.gtc md5: e001c49a6cd9cb209925fcdeecc12c57 File: 5511344027_R01C01.gtc.txt md5: 556900b8da95b49ad1c7318cc8464a45 File: 5511344027_R01C01_Grn.idat md5: 8ea4f476bdfa50234ed5aadc8e26f533 File: 5511344027_R01C01_Red.idat md5: 9b4a12b660dc101b47a977bc3bd20c9f File: 5511344027_R01C02.gtc md5: ad227c493a77b11144ff1975311d8eb2 File: 5511344027_R01C02.gtc.txt md5: 556900b8da95b49ad1c7318cc8464a45 File: 5511344027_R01C02_Grn.idat md5: 8858ec85cbd4caade2669f5a89ead2f2 File: 5511344027_R01C02_Red.idat md5: ab50d2b76fee464b265e9a3923f8cfc2 File: 5511344027_R02C01.gtc md5: d42291f1e158c1ddfe900a699130af76 File: 5511344027_R02C01.gtc.txt md5: eb54ffad24e7d62a9904b1709315f1a9 File: 5511344027_R02C01_Grn.idat md5: 7e7c546330216d9423827c16da30aeb4 File: 5511344027_R02C01_Red.idat md5: 6f8401e3cc6e87b8b662d54465a4ee10 File: 5511344027_R02C02.gtc md5: 754e35cf145c3a98a487164d98ce2d99 File: 5511344027_R02C02.gtc.txt md5: 556900b8da95b49ad1c7318cc8464a45 File: 5511344027_R02C02_Grn.idat md5: 9a5dfcb9879bcf8df1d02c697b316033 File: 5511344027_R02C02_Red.idat md5: b0f6786dad08d527f7c77b533a689975 File: 5511344027_R03C01.gtc md5: c4e9da933c3b9a40aa0447d387024d6b File: 5511344027_R03C01.gtc.txt md5: ce0be1a7dbe78e36e3fb0a56e7b5d11a File: 5511344027_R03C01_Grn.idat md5: b8481c4585a0c8e48bd42f6520fa5219 File: 5511344027_R03C01_Red.idat md5: 78cb003616051a71c229e50329f68903 File: 5511344027_R03C02.gtc md5: 93e9f6d9bbd53ce7820e6a37d0be45a8 File: 5511344027_R03C02.gtc.txt md5: eb54ffad24e7d62a9904b1709315f1a9 File: 5511344027_R03C02_Grn.idat md5: dad2e8e9c6d45e2f0a38de30d5c82e23 File: 5511344027_R03C02_Red.idat md5: df91ca7ff04bbe391b940a9087e5a52a File: 5511344027_R04C01.gtc md5: a6346d8a47ebc2677470684b89a882aa File: 5511344027_R04C01.gtc.txt md5: ce0be1a7dbe78e36e3fb0a56e7b5d11a File: 5511344027_R04C01_Grn.idat md5: 2724c95711c952bbc6c4037e8f426d72 File: 5511344027_R04C01_Red.idat md5: ff6aaacf493ccaa24e9299cef4ef3d17 File: 5511344027_R04C02.gtc md5: 82a359a733e2ff7b4e7bcdc0585122f3 File: 5511344027_R04C02.gtc.txt md5: 556900b8da95b49ad1c7318cc8464a45 File: 5511344027_R04C02_Grn.idat md5: 147fbbbfbe0e3e1f44c2a3f74954cf8c File: 5511344027_R04C02_Red.idat md5: 498460788f7b579aa725d1680e6dc11e File: 5511344027_R05C01.gtc md5: 02d6691d2a95842a0781a913614f475a File: 5511344027_R05C01.gtc.txt md5: eb54ffad24e7d62a9904b1709315f1a9 File: 5511344027_R05C01_Grn.idat md5: 4d24558d02390e4d185bf828df1409c6 File: 5511344027_R05C01_Red.idat md5: 26e5787751607cac3759645e363f8265 File: 5511344027_R05C02.gtc md5: 74cfc42ea7c9929c2ff9969feea00771 File: 5511344027_R05C02.gtc.txt md5: 1d858a240c47a63950e3fc2c3ada8c84 File: 5511344027_R05C02_Grn.idat md5: 81d89eed3a78fa7fb25ca73912b24b43 File: 5511344027_R05C02_Red.idat md5: 7faf3e249d8561a7416c4c556177672a File: 5511344027_R06C01.gtc md5: bddf3dd3fc276ef391c6fbeed63903ef File: 5511344027_R06C01.gtc.txt md5: 556900b8da95b49ad1c7318cc8464a45 File: 5511344027_R06C01_Grn.idat md5: be3dcc57f4323aed2ed3e286becf82c4 File: 5511344027_R06C01_Red.idat md5: 0b4ecd4ce164cea420bccb6831677880 File: 5511344027_R06C02.gtc md5: 768939774eaeca7e0c5ad5549b444e9b File: 5511344027_R06C02.gtc.txt md5: 1d858a240c47a63950e3fc2c3ada8c84 File: 5511344027_R06C02_Grn.idat md5: 31ac0fb269b280bc6d26bd0a48a5dd45 File: 5511344027_R06C02_Red.idat md5: 8c385ff73d6295eb1e449345e2317dfb Folder: 5511344029 File: 5511344029_R01C01.gtc md5: 4f2bb80229e4fb40f1d5c24c67d6908e File: 5511344029_R01C01.gtc.txt md5: 0d5817d7cada8d72e7fcb35e98cc3580 File: 5511344029_R01C01_Grn.idat md5: 328916f70bb2c2ea2a6d4f43cccaf747 File: 5511344029_R01C01_Red.idat md5: 5bc1ad7570b02b437c27f1eb06cd011d File: 5511344029_R01C02.gtc md5: 87056ae98f656a6054489515e9c97654 File: 5511344029_R01C02.gtc.txt md5: 4fef32fd346dea6287d31d7f8d419f03 File: 5511344029_R01C02_Grn.idat md5: e678ce2b2b1d31069c1f64aa1de30254 File: 5511344029_R01C02_Red.idat md5: 6a6993cc3f786617cdb55883215c981a File: 5511344029_R02C01.gtc md5: e9d800ac31f147eb239f08de83c0ad5b File: 5511344029_R02C01.gtc.txt md5: 5b5da506f584a7fe8de2ac597d674c91 File: 5511344029_R02C01_Grn.idat md5: 5a9f126a176093d0708045b4629abfef File: 5511344029_R02C01_Red.idat md5: cd6dfeead1e8dbfe8d21ccd92919593a File: 5511344029_R02C02.gtc md5: 97e364a382c6bae0dfda99c7ca750d12 File: 5511344029_R02C02.gtc.txt md5: 4fef32fd346dea6287d31d7f8d419f03 File: 5511344029_R02C02_Grn.idat md5: e0337ca0ec6eade487dfeb535d1310a5 File: 5511344029_R02C02_Red.idat md5: 7acc44831666f484d5c50bd62d55b57f File: 5511344029_R03C01.gtc md5: 59a740c850e559170237d44b4c33b624 File: 5511344029_R03C01.gtc.txt md5: 8a9a9aba1b4646397d2aa3da6bd18a81 File: 5511344029_R03C01_Grn.idat md5: b4877dbaf128d17040da7cea5aa109d7 File: 5511344029_R03C01_Red.idat md5: 9ec7c68100bcf8b573ead565eb177b8c File: 5511344029_R03C02.gtc md5: 459e68bcc0923cba8fb2ee3c04e32547 File: 5511344029_R03C02.gtc.txt md5: 4fef32fd346dea6287d31d7f8d419f03 File: 5511344029_R03C02_Grn.idat md5: 84324dd7c7bdd5a92d38b4c1329560fe File: 5511344029_R03C02_Red.idat md5: d5ea12d188ae97c8ff51f01211efefe9 File: 5511344029_R04C01.gtc md5: 36c32c2c1ea343ac07879f9b27190fca File: 5511344029_R04C01.gtc.txt md5: 8a9a9aba1b4646397d2aa3da6bd18a81 File: 5511344029_R04C01_Grn.idat md5: 3fe03ebd92e4253644a48b2993372de5 File: 5511344029_R04C01_Red.idat md5: 3be25f2e6b25dcb8eb9b47b44cc18760 File: 5511344029_R04C02.gtc md5: a8ab5ea34bc627af2bd961976270ab37 File: 5511344029_R04C02.gtc.txt md5: 8a9a9aba1b4646397d2aa3da6bd18a81 File: 5511344029_R04C02_Grn.idat md5: 32f134ab1b3c0dffbc05fabca1f0e7b7 File: 5511344029_R04C02_Red.idat md5: e91e23133ef785a8e9a7c1ad0e22d061 File: 5511344029_R05C01.gtc md5: 88b2a971b497a97e612e788d38bec93f File: 5511344029_R05C01.gtc.txt md5: 5b5da506f584a7fe8de2ac597d674c91 File: 5511344029_R05C01_Grn.idat md5: 5f37475bac8b7ac387d397cc45d9632c File: 5511344029_R05C01_Red.idat md5: 253c97f825d1b2b657a63e016507f711 File: 5511344029_R05C02.gtc md5: 2d7bae1c567fee258818e691ad4e5705 File: 5511344029_R05C02.gtc.txt md5: 8a9a9aba1b4646397d2aa3da6bd18a81 File: 5511344029_R05C02_Grn.idat md5: 2443f146a07f9a38cc25106dc1d9ddfd File: 5511344029_R05C02_Red.idat md5: ca7fea414e4cf776de675032c738a353 File: 5511344029_R06C01.gtc md5: da8ef738da786798c4fecd09acca1369 File: 5511344029_R06C01.gtc.txt md5: 4fef32fd346dea6287d31d7f8d419f03 File: 5511344029_R06C01_Grn.idat md5: 3a5fe0ee28b6d0aedd0a321c0b620d07 File: 5511344029_R06C01_Red.idat md5: ded3ba572c14163f56901840bea960ca File: 5511344029_R06C02.gtc md5: f2cd26b77f29cff4681ca6f7cbcc305f File: 5511344029_R06C02.gtc.txt md5: 8a9a9aba1b4646397d2aa3da6bd18a81 File: 5511344029_R06C02_Grn.idat md5: f650e5053d51c6536d018723f298f31f File: 5511344029_R06C02_Red.idat md5: 39e04dc1e819ceda6738d825fb2e477d Folder: 5500696004 File: 5500696004_R01C01.gtc md5: 19891392b956ccbccad0b7ffdccb2588 File: 5500696004_R01C01.gtc.txt md5: a035ee483e9a726e0273d50d3ac6dbc7 File: 5500696004_R01C01_Grn.idat md5: 08f25ffd4260a39d36f1a99d4313ba53 File: 5500696004_R01C01_Red.idat md5: 8fa1b53cb15763229a36b08f29451b77 File: 5500696004_R01C02.gtc md5: 4989423fc90f374ae9751d397295376c File: 5500696004_R01C02.gtc.txt md5: 82bf0e55c36f2d70a4bb463e9e18f9e2 File: 5500696004_R01C02_Grn.idat md5: 737e1df2eba96995a57aa93099129a65 File: 5500696004_R01C02_Red.idat md5: 2cf92ab78cf30bd7cc1243e83db4d647 File: 5500696004_R02C01.gtc md5: 8bd4ea07cb67fb45266a4ec1667e9e98 File: 5500696004_R02C01.gtc.txt md5: 5e00d2a80f6e0f1969066d83e2623b91 File: 5500696004_R02C01_Grn.idat md5: 5bc1c80f8d7b5f9c0879d8417d4224cb File: 5500696004_R02C01_Red.idat md5: 58ea8ca0327903a04897e880c36e8dfc File: 5500696004_R02C02.gtc md5: 02c6431895a9617f3dd52b027222f66b File: 5500696004_R02C02.gtc.txt md5: fadeed6fd278a37971ea5db831c22ede File: 5500696004_R02C02_Grn.idat md5: 287d26f4ff26c31276d61e8026cc024d File: 5500696004_R02C02_Red.idat md5: ec04c142dea85338453e85e5ba27b3a2 File: 5500696004_R03C01.gtc md5: f726c97a73f10463362068d05541872b File: 5500696004_R03C01.gtc.txt md5: a9aae587bfb74e1045d9f908c7d69a55 File: 5500696004_R03C01_Grn.idat md5: e745ef83168e91de9238f74b0bf24b46 File: 5500696004_R03C01_Red.idat md5: 362acd545f92d687afca5974ab5b6001 File: 5500696004_R03C02.gtc md5: 059d136d59134e4540e22fa1ca00ae7a File: 5500696004_R03C02.gtc.txt md5: 6dbccd8daa0a291621418fccfebdd40d File: 5500696004_R03C02_Grn.idat md5: 0a42e37b86c186421bcefe73e565c337 File: 5500696004_R03C02_Red.idat md5: 55285440e85b04a450bf714b038896cf File: 5500696004_R04C01.gtc md5: 4ed48575ec8413239608a3884cd4283f File: 5500696004_R04C01.gtc.txt md5: 2736d05434b6c4644e9317048edf1185 File: 5500696004_R04C01_Grn.idat md5: 8cb1aeb8f4a7f015844d9384245d9ab0 File: 5500696004_R04C01_Red.idat md5: 46f1f6b5fb7aceee14927a47f0a4a5e0 File: 5500696004_R04C02.gtc md5: a9f00f0a97ce66b2f086855009e98eb2 File: 5500696004_R04C02.gtc.txt md5: f13611195deb9637168f7fad67a6c673 File: 5500696004_R04C02_Grn.idat md5: 3126004a7a42b8cc9337177ba7e4c640 File: 5500696004_R04C02_Red.idat md5: 08854ff3e4f0ba2aa45833e8b01e23b9 File: 5500696004_R05C01.gtc md5: 12c6a4c7ecceaf140ee8c7e5eb0600b2 File: 5500696004_R05C01.gtc.txt md5: f5cd2f8fdc1df9668257041e8ed914d9 File: 5500696004_R05C01_Grn.idat md5: f94fb05b574c51fc3dc1f3632466fa00 File: 5500696004_R05C01_Red.idat md5: 26038e7014228cdda83d2ecd0269b61a File: 5500696004_R05C02.gtc md5: 55479940c6ffd2f0b18d0c6337591862 File: 5500696004_R05C02.gtc.txt md5: 1925df1106863d025a1880891fac5a9d File: 5500696004_R05C02_Grn.idat md5: 1a4d2010ffd0eca2c41851befd65d8cf File: 5500696004_R05C02_Red.idat md5: e9c73ea2162669b3673bf3d03a4c2030 File: 5500696004_R06C01.gtc md5: fb3a313beaa1ba980d9d3b0e856f3ac3 File: 5500696004_R06C01.gtc.txt md5: 911a8feb184575aa56b8d713bfb8cb70 File: 5500696004_R06C01_Grn.idat md5: 13c2f60b7743a94d2cd269762840edd1 File: 5500696004_R06C01_Red.idat md5: 3c7b43bf94b29f2b2e824efee4d86364 File: 5500696004_R06C02.gtc md5: d92032c3539afb02a71ecd9de1da26d8 File: 5500696004_R06C02.gtc.txt md5: c85a9a2fa58d78802863643a28bb7fe6 File: 5500696004_R06C02_Grn.idat md5: b1871e4af78f5a9a2d6c893b2434a688 File: 5500696004_R06C02_Red.idat md5: 46c3c118f2198aa8f87e2fd59c6065b5 Folder: 5500696005 File: 5500696005_R01C01.gtc md5: b10555250b0ef176760173a481cb6da2 File: 5500696005_R01C01.gtc.txt md5: 8ee2617f8e8d3b3ed66ba48945b7182c File: 5500696005_R01C01_Grn.idat md5: a674f0d110ff38bec609708883ee888c File: 5500696005_R01C01_Red.idat md5: e9bf6b677298e0fc5b92171cba04abd0 File: 5500696005_R01C02.gtc md5: 6be4da9d6acda7067723455cddb01210 File: 5500696005_R01C02.gtc.txt md5: 355115ee4bb75ba7e308a4621ada373b File: 5500696005_R01C02_Grn.idat md5: c12713141b2e998bcc39c709399dbfaf File: 5500696005_R01C02_Red.idat md5: 18c2ff9a79484d612fa0d646f5f3c435 File: 5500696005_R02C01.gtc md5: 2cb25fa26a36011a72db9bf30e32246c File: 5500696005_R02C01.gtc.txt md5: 99905c477316ba3e4a3122843b5a7e8b File: 5500696005_R02C01_Grn.idat md5: 461cb3f7100676af5e2b8051b9d35eb2 File: 5500696005_R02C01_Red.idat md5: 0d10b120b3bef162573d567ace2cec5a File: 5500696005_R02C02.gtc md5: c8c22e78905fa500ec83aca366247bfa File: 5500696005_R02C02.gtc.txt md5: e87a84e53718c37203ad3f6f63b06324 File: 5500696005_R02C02_Grn.idat md5: b674fbbeec462ea468f2ab5ba2173ed8 File: 5500696005_R02C02_Red.idat md5: 6d106644fb1a8d8b4d3f06add911cfac File: 5500696005_R03C01.gtc md5: b048d07ca2f151cb0fd6bc61ac71fd7a File: 5500696005_R03C01.gtc.txt md5: a9c65313f5c4929fd4abf4021c8a67ed File: 5500696005_R03C01_Grn.idat md5: 858e27d7393a8c38403de2467138d033 File: 5500696005_R03C01_Red.idat md5: 969c6b588ae806c1240ced1674e03efd File: 5500696005_R03C02.gtc md5: 0fc100e6075a463becc8167298668325 File: 5500696005_R03C02.gtc.txt md5: 5508e590faf14f4eecb8615858f57e0f File: 5500696005_R03C02_Grn.idat md5: 15ccedf8a52d6b13d7baccea127ddbf5 File: 5500696005_R03C02_Red.idat md5: ce2f56204001eceb69bd9290718a47ac File: 5500696005_R04C01.gtc md5: eefea0b83e93ce361d878d6bae14b9f4 File: 5500696005_R04C01.gtc.txt md5: 891200b1900b0eee1e123645edc0e939 File: 5500696005_R04C01_Grn.idat md5: 236548e1f30e4682e8d4e8149f375d1a File: 5500696005_R04C01_Red.idat md5: db3fc6573b9bbde5c830e0e8f62754d2 File: 5500696005_R04C02.gtc md5: 80db23e38a9e6fe5e80661adbe09a191 File: 5500696005_R04C02.gtc.txt md5: de9674cf3d55f82ccb4e4b03d0fb0785 File: 5500696005_R04C02_Grn.idat md5: 08e98bd7ebd14a340b39f429c7e088ad File: 5500696005_R04C02_Red.idat md5: a4b07a0f49a8cdbcb67e6adfc6e8c81a File: 5500696005_R05C01.gtc md5: 9d80a6d9f93388b410b94cb7f74858a3 File: 5500696005_R05C01.gtc.txt md5: 370ff16d493d62e709ebe7660cb0e0ca File: 5500696005_R05C01_Grn.idat md5: 109ed21d6b1b8e17cbffa8c649236dcc File: 5500696005_R05C01_Red.idat md5: 1618ee67b1e870f27f0f2dc20a1f05b4 File: 5500696005_R05C02.gtc md5: 6c526fd13c8c1043513282580c4a0381 File: 5500696005_R05C02.gtc.txt md5: 4c9de594a8ed3382ba1bd8d7248b5217 File: 5500696005_R05C02_Grn.idat md5: 3a456d4c5c245d8c1f588768f0cf2a5f File: 5500696005_R05C02_Red.idat md5: ca21220b06e0eb0e05e58be808ad64dc File: 5500696005_R06C01.gtc md5: 79ee2e611c02c290549a62f74d9dffcc File: 5500696005_R06C01.gtc.txt md5: e06d21afbb221c4efe9537c7c6c0a00c File: 5500696005_R06C01_Grn.idat md5: 109e5f2b63ecd341d3a72fe9b987bc57 File: 5500696005_R06C01_Red.idat md5: 0ac5b428a86a90fc48fa32d798136092 File: 5500696005_R06C02.gtc md5: 4b02e8a8d81f6e87f43ead8c3ebdf863 File: 5500696005_R06C02.gtc.txt md5: b21c1986b8c7c14802e4c190e330ffc0 File: 5500696005_R06C02_Grn.idat md5: c168540a9e4cc0661cf75e192cb1416b File: 5500696005_R06C02_Red.idat md5: f6aab11d4c1ff62dec8cc3707298d285 Folder: 5500696010 File: 5500696010_R01C01.gtc md5: 553e76a9895ad2327ba1bb312b062a9b File: 5500696010_R01C01.gtc.txt md5: d2073e60e8b2745bd6d8cbb13f615f19 File: 5500696010_R01C01_Grn.idat md5: b567c23767b76556a3eb99783b6a197a File: 5500696010_R01C01_Red.idat md5: 3a42e61b8e8bd3f3a149a5b5d361aa95 File: 5500696010_R01C02.gtc md5: 440d0f0a533cfc4862dfa6df801498a9 File: 5500696010_R01C02.gtc.txt md5: 32064ff42112d97717acb5b3ab316484 File: 5500696010_R01C02_Grn.idat md5: cf934e9ce467cccc2de2bbed3d8d91f8 File: 5500696010_R01C02_Red.idat md5: 04f36a9eb0e7ed37b4affd1a67dfc643 File: 5500696010_R02C01.gtc md5: 5900ca51589d800e9394fa680f63cdf5 File: 5500696010_R02C01.gtc.txt md5: 0eb638509a00bbb77b1d8b8096e4ff70 File: 5500696010_R02C01_Grn.idat md5: cafbef4c3aea4ff963acb6a647be1768 File: 5500696010_R02C01_Red.idat md5: 4e6a084e10a6ba3e287a5a70bf44a9ed File: 5500696010_R02C02.gtc md5: 6b5ba8e2cc959573450466e831730071 File: 5500696010_R02C02.gtc.txt md5: 0ef78c9c87c0902f7a988e46783961b2 File: 5500696010_R02C02_Grn.idat md5: 5acbaf62b45bbe44bff16f30ed20091d File: 5500696010_R02C02_Red.idat md5: 7aeaf52bc474e96eb1d406b1eb19e61e File: 5500696010_R03C01.gtc md5: 60b9528a337e18784d657130b2f0cbe2 File: 5500696010_R03C01.gtc.txt md5: 641155cb2003442cc9156366515d3e60 File: 5500696010_R03C01_Grn.idat md5: 801dda4516050749a694153ea0f32e6b File: 5500696010_R03C01_Red.idat md5: b5b4041ecaddb3470daa1405893ba7aa File: 5500696010_R03C02.gtc md5: e137e128cf1a174b833a873ca337456f File: 5500696010_R03C02.gtc.txt md5: 2827246fe5d8712ed111df4d70992c76 File: 5500696010_R03C02_Grn.idat md5: 048236c2a207d0627e421eeea9ac4ca8 File: 5500696010_R03C02_Red.idat md5: 7cb81bf60d3d8240fd59a987ca3b4f9c File: 5500696010_R04C01.gtc md5: 781cbc7cf76f36b7a0f145b35d892229 File: 5500696010_R04C01.gtc.txt md5: 630a200a41776ea264a90bbcae630ade File: 5500696010_R04C01_Grn.idat md5: a95dd6f22c19e682f2e2d9ceecba80c2 File: 5500696010_R04C01_Red.idat md5: 8889a3b9dd3684b16a4c0c8e13ec66c5 File: 5500696010_R04C02.gtc md5: a9d7560bdcb95a675da59dee2dfac800 File: 5500696010_R04C02.gtc.txt md5: b4446592e100b7e3e25d03905c11f851 File: 5500696010_R04C02_Grn.idat md5: 63a41144565a8151186f779a25bfa4fd File: 5500696010_R04C02_Red.idat md5: a509c7d902eab06742195bea89990640 File: 5500696010_R05C01.gtc md5: 8c7ddb26555bc6e3f9d0226311e5e112 File: 5500696010_R05C01.gtc.txt md5: c0865d90007dc975e8567359bceffb98 File: 5500696010_R05C01_Grn.idat md5: bc294db8cc316fe0835ad278444c0ee8 File: 5500696010_R05C01_Red.idat md5: d898f5a822db25f19727a08177aa5333 File: 5500696010_R05C02.gtc md5: a92a004b0ded220bb201a9ea144561bf File: 5500696010_R05C02.gtc.txt md5: 808c14670a8041397ed7acb833b41e08 File: 5500696010_R05C02_Grn.idat md5: f707a811ae660e60b51c2a94aab5eaa9 File: 5500696010_R05C02_Red.idat md5: e0cd21c7c65649604d58f3c696e87578 File: 5500696010_R06C01.gtc md5: 5bb7d42acc520e625ba811d5e11ba196 File: 5500696010_R06C01.gtc.txt md5: 217b774f1a4e3574d5d3bdce617a9f13 File: 5500696010_R06C01_Grn.idat md5: b7a6e0b07857f89805f56e82d1d79c54 File: 5500696010_R06C01_Red.idat md5: 48cedd080f3ebb428e8d5ee8599670ca File: 5500696010_R06C02.gtc md5: 36dec01e234a1f52f9bea9036861afb6 File: 5500696010_R06C02.gtc.txt md5: da6d6f2995bc380bd1965fdb510fe476 File: 5500696010_R06C02_Grn.idat md5: b21f5ce09253f44c19b46d88be99aa14 File: 5500696010_R06C02_Red.idat md5: 84ee94edf1c5198b4ee2c00b3b80feec Folder: 5500696014 File: 5500696014_R01C01.gtc md5: e75e5d24a216edaeca296e1a6c3ba14d File: 5500696014_R01C01.gtc.txt md5: 63936af83a5319490a3406e32686f728 File: 5500696014_R01C01_Grn.idat md5: b720f34df3472d1206f15f9d1262529f File: 5500696014_R01C01_Red.idat md5: dcc458bdae1d3d56fb8751599a257555 File: 5500696014_R01C02.gtc md5: 26701f8e96572c5a1e7e1dd1fea0586c File: 5500696014_R01C02.gtc.txt md5: 8f6941daf79ba1b8e4f2915d80d594ec File: 5500696014_R01C02_Grn.idat md5: 8d450ca1d464211b5b2442b1b464b0c6 File: 5500696014_R01C02_Red.idat md5: aeb1d961a37216013794866379204c37 File: 5500696014_R02C01.gtc md5: ebb60962564c41292c8f8bc02aad215f File: 5500696014_R02C01.gtc.txt md5: 9c33ac253439c04ee6f9ae39c6a2a549 File: 5500696014_R02C01_Grn.idat md5: b668cde1c821ed8ee31ee63393b89f1e File: 5500696014_R02C01_Red.idat md5: c6423c5260c8a1bbbfbcdf904b287acf File: 5500696014_R02C02.gtc md5: 5c012c678a3384cae0225489da42473b File: 5500696014_R02C02.gtc.txt md5: 239cc6489243d2d586e318d34197d835 File: 5500696014_R02C02_Grn.idat md5: b46a0832454c670d3bd009e62a8545cb File: 5500696014_R02C02_Red.idat md5: f37fb223640ff05ea67e03b3ebb75d8d File: 5500696014_R03C01.gtc md5: e0f131c67915b2a2195eca054ad064f2 File: 5500696014_R03C01.gtc.txt md5: b5bcd55b982433b873286cb020657d05 File: 5500696014_R03C01_Grn.idat md5: a67670036ebb0e110d1162c4d6235763 File: 5500696014_R03C01_Red.idat md5: db2dcc2d7bbce43c37d0fdf7563b3d22 File: 5500696014_R03C02.gtc md5: b61c528e980e305ce1b38ff590926424 File: 5500696014_R03C02.gtc.txt md5: 95af98f46f697cc6831b04202ec97b87 File: 5500696014_R03C02_Grn.idat md5: bc86384b741f473d7e4a388702698ed4 File: 5500696014_R03C02_Red.idat md5: b77f1e805f2bf6bcc86b7dc3a243455a File: 5500696014_R04C01.gtc md5: e0034e00e75986cd1ecacdfea19d9b91 File: 5500696014_R04C01.gtc.txt md5: 9f0ea74a9df964408dbf6269ba28ce94 File: 5500696014_R04C01_Grn.idat md5: 0d09148a8cae9a155b819314388689a7 File: 5500696014_R04C01_Red.idat md5: 906d4f6858a790624828f814fb8d4471 File: 5500696014_R04C02.gtc md5: 95050add386aafdae1b2d80a2e450d79 File: 5500696014_R04C02.gtc.txt md5: e954e18243778b2ba2fecf9c3cb26c4c File: 5500696014_R04C02_Grn.idat md5: bae414e44ac5e07a3fa02de2b2435377 File: 5500696014_R04C02_Red.idat md5: bfc5b46233925811bc50c0ef1e519f4e File: 5500696014_R05C01.gtc md5: a9e3684211f3c191b19076598d1dd9da File: 5500696014_R05C01.gtc.txt md5: 9c0dd0be78af94785869663523f37879 File: 5500696014_R05C01_Grn.idat md5: ee9fba8dfff9dcfca58617974b29c429 File: 5500696014_R05C01_Red.idat md5: e5294b7f0237e02b9c939acf9220e735 File: 5500696014_R05C02.gtc md5: fe97fb8dcbbded4a7ed688530a545144 File: 5500696014_R05C02.gtc.txt md5: c8d96cb1f50b5e5d1a3d88b5d1d5b97b File: 5500696014_R05C02_Grn.idat md5: 61ea3d3c3bce97b725a8a4cff3f3f95a File: 5500696014_R05C02_Red.idat md5: 9cd50edd38c49053a2fa7e44828c657f File: 5500696014_R06C01.gtc md5: 7459425a85ed68e757f354e3ebd52671 File: 5500696014_R06C01.gtc.txt md5: 542ae551352d9c4d3434e0da00d1b119 File: 5500696014_R06C01_Grn.idat md5: 1c2f701e0e699a68c698ee08b7a58109 File: 5500696014_R06C01_Red.idat md5: 538f1d305a05fc9cd726184ad76ebd0f File: 5500696014_R06C02.gtc md5: ee20c63f342894a43233f5c000aae056 File: 5500696014_R06C02.gtc.txt md5: a499b6d3df71cd2f33a1aab06e34e2dd File: 5500696014_R06C02_Grn.idat md5: 63c0076823fd20d970e8741e53e759d2 File: 5500696014_R06C02_Red.idat md5: 72681febae31e11b8e3eee408c940213 FILE: MW.ped MD5SUM: 833cd6a9e7af3403938fea1cd42a4dac DESCRIPTION: This file contains the initial, unedited genotypes and sample information for the 96 samples (95 Mex Wolves, including replicates and 1 domestic dog). The format is in the standard PLINK ped format. FORMAT: ped FILE: MW.map MD5SUM: 319a4caec5ca64bb49c07648d805ea2a DESCRIPTION: This file contains the SNP position data in the Plink 'map' format for the 172114 raw SNPs before cleaning but after initial removal of SNPs with low GenTrain score using Illumina's GenomeStudio software. FORMAT: map FILE: MW-Samples.xlsx MD5SUM: fc598b76ca3309049b28a60fc806e190 DESCRIPTION: This is a Microsoft Excel-formatted spreadsheet containing the identification and source of the 96 samples used. Use this file to convert IDs between the beadchip position and Mexican Wolf studbook ID. Samples were collected from the Museum of Southwestern Biology (MSB, see OTHER_ID column for Museum voucher ID). FORMAT: xlsx FILE: MW.clean.ped MD5SUM: 8b4b43eb7a667fe365b6bb4aebfb17fe DESCRIPTION: This file contains the filtered set of genotypes and sample information for the 84 samples (83 Mex Wolves and 1 domestic dog). See Table 1 in the manuscript. The format is in the standard PLINK ped format. FORMAT: ped FILE: MW.clean.map MD5SUM: fb51e8bb98ee5256aad847e444efab79 DESCRIPTION: This file contains the SNP position data in the Plink 'map' format for the 62219 SNPs after filtering. See Table 1 in the manuscript FORMAT: map FILE: MERGED.ped MD5SUM: 6c792c6ecbd227fff42bd755ea6c57ec DESCRIPTION: This file contains the unfiltered set of genotypes and sample information for the 1094 samples (89 Mex Wolves + 371 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format. FORMAT: ped FILE: MERGED.map MD5SUM: 055257651f2853ee47b071e350f84ddc DESCRIPTION: This file contains the SNP position data in the Plink 'map' format for the 169066 SNPs before filtering. See Table 1 in the manuscript FORMAT: map FILE: MERGED.clean.ped MD5SUM: 4e08b2a5832cbb7bad1fa7ef0b7cdf83 DESCRIPTION: This file contains the filtered set of genotypes and sample information for the 1021 samples (88 Mex Wolves + 299 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format. FORMAT: ped FILE: MERGED.clean.map MD5SUM: 4a177fdf67ba10539a45984f6ed0c6fd DESCRIPTION: This file contains the SNP position data in the Plink 'map' format for the 118287 SNPs after filtering. See Table 1 in the manuscript FORMAT: map FILE: MERGED.clean.pruned.ped MD5SUM: d77c5d250fca374bcabb13e435133f36 DESCRIPTION: This file contains the filtered set of genotypes and sample information for the 1021 samples (88 Mex Wolves + 299 gray wolves + 634 domestic dogs). See Table 1 in the manuscript. The format is in the standard PLINK ped format. FORMAT: ped FILE: MERGED.clean.pruned.map MD5SUM: b9577a45c5fe4dc3fd846176ced78ef8 DESCRIPTION: This file contains the SNP position data in the Plink 'map' format for the 74876 SNPs after filtering and LD pruning. See Table 1 in the manuscript FORMAT: map FILE: LampLD-3way.tar.gz MD5SUM: 4d60ef80a77328ba261f26f8860137ce DESCRIPTION: This file, once unpacked, contains the results of the local ancestry analysis using LAMP-LD v1.3. In addition to the numerous output files, there is a folder for each of the 38 chromosomes. Each chromosome's folder contains the LAMP-LD results. Most importantly, for each chromosome the phased genotypes generated using Beagle are found in the files chr#_phased.txt. I recommend following the code described at the GitHub page https://github.com/rfitak/Mexican_Wolf_SNPs to know exactly what each of the files represents. FORMAT: tar.gz #################################################### ############ Appendix 1: File Formats ############# #################################################### Format: tar.gz The format represents a folder of files that have been archived together (.tar) then compressed (.gz). Most computers can unpack this file into a folder of files by double-clicking automatically. In most unix machines, it can easily be unpacked from the command line using: tar -zxvf file.tar.gz Format: ped/map This format is one of the standard representations of SNP genotypes. The sample information and genotypes are provided in the 'map' file, whereas the mapping information for each SNP is found in the 'map' file. Also referred to as 'Plink' format, see the link below for a complete description. http://zzz.bwh.harvard.edu/plink/data.shtml Format: xlsx This format stores tabulated data for use in spreadsheet software, e.g. MS Excel