and BeadChip platforms.Selected SNPs are located close to each other within 500 bp window length (reasonable limit of one Sanger read).Specific primers can be selected for these SNPs-containing region (by Primer-BLAST [7]).Table 4The chosen regions for validation by Sanger sequencing for sample_002ChromosomeStartEndINDELsSNVsTotalGenotypesVartypeBeadChipWGS1109711850109712150033TGGG3 SNVsTCTTCGGG1109759300109759400101DDII1 INDEL28566360085663700101DIII1 INDEL2233671750233671850101IIDI1 INDEL6160246180160246690033GGAA3 SNVsTTCCGGAA10101010500101010600101DDII1 INDEL134979250049792600101DDDI1 INDEL223797380037974170101DDII1 INDELTable 5The designed primers for amplification and sequencing of the chosen regionsChromosomeOrientationNameSequence 5′3’LengthTmGCStartEndAmplifying lengthN mismatchesMismatch type1Fchr1_reg1_FAAGCCCTCGGAGTAGCTTTC2059.465510971175510971177439733 SNV1Rchr1_reg1_RGGCTGGAATCAATAAGCCCC2058.675510971215110971213239733 SNV1Fchr1_reg2_FTGATGGACAGGATGGAGTTGTAG2359.5547.831097593001097593228511 INDEL1Rchr1_reg2_RGAGCTGGACTCTTACCGCCTA2161.0257.141097593841097593648511 INDEL2Fchr2_reg1_FGTGGTCACGGACATGCAGA1960.0157.89856634288566344634411 INDEL2Rchr2_reg1_RCTGAGCGCTACTCCGTCATC2060.3260.00856637718566375234411 INDEL2Fchr2_reg2_FCTCTGGACAGAGAGTATTTGGTTG2458.8345.8323367151023367153337011 INDEL2Rchr2_reg2_RAGGTGGGAGAAATACCAGCAC2159.7252.3823367187923367185937011 INDEL6Fchr6_FTTTAAGAAGGCAGGGGATTGCT2259.9645.4516024643116024645249033 SNV6Rchr6_RGCAACTTAAGCCTTCACCAGT2158.7747.6216024692016024690049033 SNV10Fchr10_FCCTGGAGACTTGCCTTGACC2060.326010101051110101053023311 INDEL10Rchr10_RCCTCTACAAGACGTGCCAGT2059.405510101074310101072423311 INDEL13Fchr13_FAAGCTCTTGATGCGGTGGTT2060.2550497924634979248233011 INDEL13Rchr13_RCACGTATAGCCCGGCGAA1859.5961.11497927924979277533011 INDEL22Fchr22_FCGAGGGCCCCATATAGGAGA2059.9660379736033797362240811 INDEL22Rchr22_RGAGTTGGACCAGTACCTGCC2060.0460379740103797399140811 INDEL
