This README.txt file was generated on 06/16/2022 by Xiang Li GENERAL INFORMATION 1. Title of Dataset: Iberian_weedy_rice.vcf 2. Author Information A. Principal Investigator Contact Information Name: Ana Caicedo Institution: University of Massachusetts Address: 611 N. Pleasant St, Amherst, MA 01003 Email: caicedo@umass.edu B. Associate or Co-investigator Contact Information Name: Xiang Li Institution: University of Massachusetts Address: 611 N. Pleasant St, Amherst, MA 01003 Email: xli4@umass.edu C. Alternate Contact Information Name: Institution: Address: Email: 3. Date of data collection (single date, range, approximate date) : NA 4. Geographic location of data collection: Spain and Portugal 5. Information about funding sources that supported the collection of the data: NSF IOS-1032023 and NSF IOS-1947609 SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: NA 2. Links to publications that cite or use the data: https://doi.org/10.1002/ppp3.10286 3. Links to other publicly accessible locations of the data: NA 4. Links/relationships to ancillary data sets: Raw reads for Genotyping by Sequencing (GBS) are openly available in the NCBI Short Read Archive (SRA) under IDs SRR17766549 to SRR17766467. 5. Was data derived from another source? no 6. Recommended citation for this dataset: NA DATA & FILE OVERVIEW 1. File List: Iberian_weedy_rice.vcf 2. Relationship between files, if important: NA 3. Additional related data collected that was not included in the current data package: NA 4. Are there multiple versions of the dataset? no METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: details in the publication. 2. Methods for processing the data: details in the publication. 3. Instrument- or software-specific information needed to interpret the data: text editor or vcftools 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: NA 6. Describe any quality-assurance procedures performed on the data: details in the publication 7. People involved with sample collection, processing, analysis and/or submission: Xiang Li, Shulin Zhang DATA-SPECIFIC INFORMATION FOR Iberian_weedy_rice.vcf 1. Number of variables: 481 2. Number of cases/rows: NA 3. Variable List: ID Oryza type 1107 Cultivar 5803 Cultivar 16428 Cultivar 16657 Cultivar 27016 Cultivar 40748 Cultivar 52696 Cultivar 54287 Cultivar 62151 Cultivar 64519 Cultivar 64598 Cultivar 66069 Cultivar 66158 Cultivar 71333 Cultivar 71389 Cultivar 71481 Cultivar 71482 Cultivar 71483 Cultivar 71498 Cultivar 71500 Cultivar 71521 Cultivar 71547 Cultivar 71550 Cultivar 71563 Cultivar 71564 Cultivar 71586 Cultivar 71615 Cultivar 71634 Cultivar 71653 Cultivar 71655 Cultivar 73222 Cultivar 77579 Cultivar 78592 Cultivar 78594 Cultivar 78597 Cultivar 78599 Cultivar 79154 Cultivar 79552 Cultivar 79803 Cultivar 79805 Cultivar 79817 Cultivar 79820 Cultivar 79821 Cultivar 79829 Cultivar 80470 Wild rice 80724 Wild rice 81883 Wild rice 81990 Wild rice 82037 SE Asian weedy rice 82687 Cultivar 82691 Cultivar 83850 Cultivar 86449 SE Asian weedy rice 86478 South Asian weedy rice 86494 Wild rice 88001 Cultivar 88834 Wild rice 89191 SE Asian weedy rice 89235 SE Asian weedy rice 89240 SE Asian weedy rice 90675 Cultivar 90705 Cultivar 90734 NE Asian weedy rice 90740 NE Asian weedy rice 90752 NE Asian weedy rice 90754 NE Asian weedy rice 90785 NE Asian weedy rice 90818 NE Asian weedy rice 90819 NE Asian weedy rice 90822 NE Asian weedy rice 90835 NE Asian weedy rice 99599 SE Asian weedy rice 99601 SE Asian weedy rice 100206 South Asian weedy rice 100218 SE Asian weedy rice 100916 Wild rice 101974 Wild rice 102157 SE Asian weedy rice 103423 Wild rice 103821 Wild rice 103830 Wild rice 104406 SE Asian weedy rice 104455 SE Asian weedy rice 104496 SE Asian weedy rice 104501 Wild rice 104599 Wild rice 104624 Wild rice 104764 Wild rice 104812 Wild rice 104875 Wild rice 105353 SE Asian weedy rice 105362 SE Asian weedy rice 105706 Wild rice 105709 Wild rice 105720 Wild rice 105728 SE Asian weedy rice 105798 SE Asian weedy rice 105851 Wild rice 105855 Wild rice 105888 Wild rice 105898 Wild rice 105942 Wild rice 106086 Wild rice 106097 South Asian weedy rice 106103 Wild rice 106122 Wild rice 106126 Wild rice 106134 Wild rice 106166 Wild rice 106168 Wild rice 106169 Wild rice 106316 SE Asian weedy rice 106321 Wild rice 106332 SE Asian weedy rice 106338 SE Asian weedy rice 106431 SE Asian weedy rice 106453 Wild rice 106518 Wild rice 109634 Cultivar 112801 NE Asian weedy rice 112821 NE Asian weedy rice 112832 NE Asian weedy rice 113866 NE Asian weedy rice 115190 Cultivar 115298 NE Asian weedy rice 115306 NE Asian weedy rice 115580 NE Asian weedy rice 117123 NE Asian weedy rice 117124 NE Asian weedy rice BG17 SE Asian weedy rice BG20 SE Asian weedy rice BG22 SE Asian weedy rice GSOR-301011 Cultivar GSOR-301069 Cultivar GSOR-301070 Cultivar GSOR-301095 Cultivar GSOR-301097 Cultivar GSOR-301123 Cultivar GSOR-301144 Cultivar GSOR-301169 Cultivar GSOR-301199 Cultivar GSOR-301201 Cultivar GSOR-301251 Cultivar GSOR-301252 Cultivar GSOR-301274 Cultivar GSOR-301288 Cultivar GSOR-301303 Cultivar GSOR-301304 Cultivar GSOR-301305 Cultivar GSOR-301312 Cultivar GSOR-301313 Cultivar GSOR-301315 Cultivar GSOR-301316 Cultivar GSOR-301317 Cultivar GSOR-301318 Cultivar GSOR-301319 Cultivar GSOR-301326 Cultivar GSOR-301328 Cultivar GSOR-301329 Cultivar GSOR-301331 Cultivar GSOR-301335 Cultivar GSOR-301336 Cultivar GSOR-301341 Cultivar GSOR-301342 Cultivar GSOR-301343 Cultivar GSOR-301344 Cultivar GSOR-301345 Cultivar GSOR-301356 Cultivar GSOR-301357 Cultivar GSOR-301359 Cultivar GSOR-301363 Cultivar GSOR-301382 Cultivar GSOR-301390 Cultivar GSOR-312012 Cultivar GSOR-312016 Cultivar GSOR-312017 Cultivar IRGC-100915 South Asian weedy rice IRGC-100923 Wild rice IRGC-105696 Wild rice IRGC-109364 Cultivar IRGC-110311 Cultivar IRGC-16163 Cultivar IRGC-61895 Cultivar IRGC-61899 Cultivar IRGC-61902 Cultivar IRGC-61923 Cultivar IRGC-80737 Wild rice IRGC-80759 Wild rice IRGC-81941 Wild rice IRGC-83301 Cultivar IRGC-83344 Cultivar IRGC-93214 Wild rice IRGC-93215 Wild rice IRGC-93217 Wild rice IRGC-93219 Wild rice IRGC-93285 Wild rice IRGC-99545 Wild rice IRRI-100200 South Asian weedy rice IRRI-103790 South Asian weedy rice IRRI-103791 South Asian weedy rice IRRI-103826 South Asian weedy rice IRRI-103829 South Asian weedy rice IRRI-103832 South Asian weedy rice IRRI-103833 South Asian weedy rice IRRI-103834 South Asian weedy rice IRRI-103842 South Asian weedy rice IRRI-105311 South Asian weedy rice IRRI-105330 South Asian weedy rice IRRI-105337 South Asian weedy rice IRRI-105341 South Asian weedy rice IRRI-105343 South Asian weedy rice IRRI-105351 South Asian weedy rice IRRI-105869 South Asian weedy rice IRRI-105874 South Asian weedy rice IRRI-105877 South Asian weedy rice IRRI-105880 South Asian weedy rice IRRI-105892 South Asian weedy rice IRRI-105907 South Asian weedy rice IRRI-106030 South Asian weedy rice IRRI-106032 South Asian weedy rice IRRI-106043 South Asian weedy rice IRRI-106076 South Asian weedy rice IRRI-106120 South Asian weedy rice IRRI-106137 South Asian weedy rice IRRI-106228 South Asian weedy rice IRRI-106401 South Asian weedy rice IRRI-32399 Cultivar IRRI-33888 Cultivar IRRI-45011 Cultivar IRRI-58286 Cultivar IRRI-6663 Cultivar IRRI-74723 South Asian weedy rice IRRI-80539 South Asian weedy rice IRRI-80568 South Asian weedy rice IRRI-80591 South Asian weedy rice IRRI-80614 South Asian weedy rice IRRI-80626 South Asian weedy rice IRRI-80723 South Asian weedy rice IRRI-80741 South Asian weedy rice IRRI-81902 South Asian weedy rice IRRI-81908 South Asian weedy rice IRRI-81910 South Asian weedy rice IRRI-81914 South Asian weedy rice IRRI-81924 South Asian weedy rice IRRI-81929 South Asian weedy rice IRRI-82008 South Asian weedy rice IRRI-83256 South Asian weedy rice IRRI-86477 South Asian weedy rice IRRI-86478 South Asian weedy rice IRRI-93178 South Asian weedy rice IRRI-93179 South Asian weedy rice IRRI-93189 South Asian weedy rice IRRI-93293 South Asian weedy rice IRRI-93297 South Asian weedy rice IRRI-93302 South Asian weedy rice IRRI-93303 South Asian weedy rice IRRI-93305 South Asian weedy rice IRRI-93307 South Asian weedy rice IRRI-93313 South Asian weedy rice IRRI-93320 South Asian weedy rice KS02 SE Asian weedy rice KS05 SE Asian weedy rice MG04 SE Asian weedy rice MG06 SE Asian weedy rice MG20 SE Asian weedy rice MK09 SE Asian weedy rice MK10 SE Asian weedy rice MS15 SE Asian weedy rice MS18 SE Asian weedy rice MUSC001 SE Asian weedy rice MUSC007 SE Asian weedy rice MUSC012 SE Asian weedy rice MUSC017 SE Asian weedy rice MUSC023 SE Asian weedy rice MUSC026 SE Asian weedy rice MUSC032 SE Asian weedy rice MUSC038 SE Asian weedy rice MUSC043 SE Asian weedy rice MUSC052 SE Asian weedy rice MUSC055 SE Asian weedy rice MUSC060 SE Asian weedy rice MUSC062 SE Asian weedy rice MUSC065 SE Asian weedy rice MUSC067 SE Asian weedy rice MUSC069 SE Asian weedy rice MUSC072 SE Asian weedy rice MUSC079 SE Asian weedy rice MUSC081 SE Asian weedy rice MUSC086 SE Asian weedy rice MUSC098 SE Asian weedy rice MUSC100 SE Asian weedy rice MUSC103 SE Asian weedy rice MUSC106 SE Asian weedy rice MUSC110 SE Asian weedy rice MUSC114 SE Asian weedy rice MUSC117 SE Asian weedy rice MUSC119 SE Asian weedy rice MUSC122 SE Asian weedy rice MUSC128 SE Asian weedy rice MUSC132 SE Asian weedy rice MUSC134 SE Asian weedy rice MUSC136 SE Asian weedy rice MUSC138 SE Asian weedy rice MUSC141 SE Asian weedy rice MUSC142 SE Asian weedy rice MUSC143 SE Asian weedy rice MUSC145 SE Asian weedy rice MUSC146 SE Asian weedy rice MUSC150 SE Asian weedy rice MUSC154 SE Asian weedy rice MUSC161 SE Asian weedy rice MUSC171 SE Asian weedy rice MUSC177 SE Asian weedy rice MUSC178 SE Asian weedy rice MUSC187 SE Asian weedy rice MUSC188 SE Asian weedy rice MUSC200 Wild rice MUSC201 Wild rice MUSC202 Wild rice MUSC203 Wild rice MUSC207 Wild rice MUSC208 Wild rice MUSC209 Wild rice MUSC218 Cultivar MUSC219 Cultivar MUSC220 Cultivar MUSC221 Cultivar MUSC225 SE Asian weedy rice MUSC232 SE Asian weedy rice MUSC234 SE Asian weedy rice MUSC235 SE Asian weedy rice MUSC237 SE Asian weedy rice NT01 SE Asian weedy rice NT05 SE Asian weedy rice RR01 US weedy rice (SH) RR02 US weedy rice (BHA2) RR03 US weedy rice (BHA2) RR04 US weedy rice (SH) RR05 US weedy rice (BHA1) RR13 US weedy rice (BHA2) RR15 US weedy rice (SH) RR16 US weedy rice (BHA1) rr20 US weedy rice (BHA1) RR21 US weedy rice (BHA1) RR24 US weedy rice (BHA1) RR25 US weedy rice (BHA2) RR29 US weedy rice (BHA2) RR42 US weedy rice (SH) RR44 US weedy rice (BHA1) RR51 US weedy rice (SH) rr9 US weedy rice (SH) sar01 Cultivar sar02 Cultivar sar03 Cultivar sau01 Cultivar sau02 Cultivar sau03 Cultivar sau04 Cultivar sau07 Cultivar sin02 Cultivar sin03 Cultivar sin04 Cultivar sin9 Cultivar str04 Cultivar str10 Cultivar SUS02 US Cultivar SUS03 US Cultivar SUS04 US Cultivar SUS05 US Cultivar SUS06 US Cultivar SUS08 US Cultivar SUS09 US Cultivar SUS11 US Cultivar SUS12 US Cultivar TA06 SE Asian weedy rice TA10 SE Asian weedy rice TA22 SE Asian weedy rice TS09 SE Asian weedy rice TS15 SE Asian weedy rice TW05 SE Asian weedy rice TW13 SE Asian weedy rice TW16 SE Asian weedy rice 101148 Outgroup 104081 Outgroup 104119 Outgroup IRGC_93261 Outgroup AN-08-1 Iberian cultivar AN-08-5 Iberian cultivar AN-08-6 Iberian cultivar AN-08-8 Iberian cultivar AN-08-9 Iberian cultivar AN-09-1 Iberian cultivar AN-09-13 Iberian cultivar AN-09-17 Iberian cultivar AN-09-22 Iberian cultivar AN-09-24 Iberian cultivar AN-09-27 Iberian cultivar AN-09-3 Iberian cultivar AN-09-30 Iberian cultivar AN-09-31 Iberian cultivar AN-09-34 Iberian cultivar AN-09-36 Iberian cultivar AN-09-38 Iberian cultivar AN-09-40 Iberian cultivar AN-09-43 Iberian cultivar AN-09-46 Iberian cultivar AN-09-7 Iberian cultivar AS-09-103 Iberian weedy rice ASF-08-48 Iberian weedy rice ASF-08-49 Iberian weedy rice ASF-08-52 Iberian weedy rice ASF-09-12 Iberian weedy rice ASF-09-14 Iberian weedy rice ASF-09-21 Iberian weedy rice ASF-09-24 Iberian weedy rice ASF-09-27 Iberian weedy rice ASF-09-29 Iberian weedy rice ASF-09-33 Iberian weedy rice ASF-09-36 Iberian weedy rice ASF-09-38 Iberian weedy rice ASF-09-3 Iberian weedy rice ASF-09-7 Iberian weedy rice AS-08-17 Iberian weedy rice AS-09-118 Iberian weedy rice AS-09-123 Iberian weedy rice AS-09-135 Iberian weedy rice AS-09-137 Iberian weedy rice AS-09-147 Iberian weedy rice AS-09-155 Iberian weedy rice AS-09-156 Iberian weedy rice AS-09-162 Iberian weedy rice AS-09-1 Iberian weedy rice AS-09-33 Iberian weedy rice AS-09-38 Iberian weedy rice AS-09-49 Iberian weedy rice AS-09-7 Iberian weedy rice AS-09-90 Iberian weedy rice AS-09-93 Iberian weedy rice AS-09-96 Iberian weedy rice AS-11-1 Iberian weedy rice ASF-09-10 Iberian weedy rice AS-09-104 Iberian weedy rice AS-09-105 Iberian weedy rice AS-09-56 Iberian weedy rice AS-09-57 Iberian weedy rice ASF-08-50 Iberian weedy rice ASF-09-19 Iberian weedy rice ASF-09-23 Iberian weedy rice ASF-09-43 Iberian weedy rice ASF-09-45 Iberian weedy rice ASF-09-48 Iberian weedy rice ASF-09-54 Iberian weedy rice ASF-09-56 Iberian weedy rice ASF-09-58 Iberian weedy rice ASF-09-61 Iberian weedy rice ASF-09-6 Iberian weedy rice AS-08-13i Iberian weedy rice AS-08-29 Iberian weedy rice AS-08-37e Iberian weedy rice AS-08-4e Iberian weedy rice AS-08-6d Iberian weedy rice AS-09-115 Iberian weedy rice AS-09-129 Iberian weedy rice AS-09-131 Iberian weedy rice AS-09-148 Iberian weedy rice AS-09-14 Iberian weedy rice AS-09-16 Iberian weedy rice AS-09-19 Iberian weedy rice AS-09-29 Iberian weedy rice AS-09-3 Iberian weedy rice AS-09-54 Iberian weedy rice AS-09-58 Iberian weedy rice AS-09-65 Iberian weedy rice AS-09-68 Iberian weedy rice AS-09-74 Iberian weedy rice AS-09-76 Iberian weedy rice AS-09-88 Iberian weedy rice AS-08-25 Iberian weedy rice AS-08-8 Iberian weedy rice AS-09-134 Iberian weedy rice AS-09-70 Iberian weedy rice 4. Missing data codes: NA 5. Specialized formats or other abbreviations used: NA