msisensor-pro
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xjtu-omics
The MSI loci both in output.prefix_germline and output.prefix_somatic
when use msisensor or msisensor-pro msi to analyze the tumor-normal pair data , some MSI loci both in output.prefix_germline and output.prefix_somatic，such as: CRC_16_germline chr1 151196702 GATTG 9 T CCCCC 9|9 chr1 151196711 TTTTT 6 C TAGCA 6|6 chr1 200594041 AACAA 8 T AAGGC 8|8 chr2 148683685 TGCAT 8 A GAGGC 8|8 chr3 51417603 TGATA 7 C AGCCC 7|7 chr7 55273591 ATTTG 13 A GTATA 14|14 chr7 74608740 ACTGC 13 T ATGGT 13|13 chr7 143003662 TTTTT 19 A CTTCC 19|19 chr8 7346866 GTCCC 9 T GGTGG 9|9 chr8 7679727 CCACC 9 A GGGAC 9|9 chr11 120350636 ATATG 8 T CCCCC 8|8 chr11 120350644 TTTTT 5 C TCCTT 5|5 chr16 14983091 GAGTT 9 A CCCAT 9|9 chr16 56718015 CTGGA 20 T GTACA 19|19 chr17 56435160 AGGGA 7 C GCCTT 7|7
CRC_16_somatic chr17 56435160 AGGGA 7 C GCCTT 0.67666 1e-14 2.4e-13 1 chr16 56718015 CTGGA 20 T GTACA 0.94734 1e-14 1.2e-13 2 chr16 14983091 GAGTT 9 A CCCAT 0.040581 1e-14 8e-14 3 chr14 23652346 TTGCT 21 A GGCCA 0.98116 1e-14 6e-14 4 chr11 125490765 GAAGA 21 T AATAT 0.84764 1e-14 4.8e-14 5 chr11 120350636 ATATG 8 T CCCCC 0.031458 1e-14 4e-14 6 chr11 102193508 CTGGT 26 A GCCAC 0.87536 1e-14 3.4286e-14 7 chr8 7679727 CCACC 9 A GGGAC 0.74167 1e-14 3e-14 8 chr8 7346866 GTCCC 9 T GGTGG 0.74167 1e-14 2.6667e-14 9 chr7 143003662 TTTTT 19 A CTTCC 0.73456 1e-14 2.4e-14 10 chr7 143003342 AAGAC 25 T GAGAC 0.95439 1e-14 2.1818e-14 11 chr7 74608740 ACTGC 13 T ATGGT 0.8415 1e-14 2e-14 12 chr7 55273591 ATTTG 13 A GTATA 0.97535 1e-14 1.8462e-14 13 chr4 55598211 TTTGA 25 T GAGAA 0.98916 1e-14 1.7143e-14 14 chr3 51417603 TGATA 7 C AGCCC 0.71456 1e-14 1.6e-14 15 chr2 148683685 TGCAT 8 A GAGGC 0.99445 1e-14 1.5e-14 16 chr2 95849361 TCCTA 23 T GTGAG 0.87912 1e-14 1.4118e-14 17 chr2 47641559 CAGGT 27 A GGGTT 0.99225 1e-14 1.3333e-14 18 chr2 39564893 TCCAG 28 T GAGAC 0.90117 1e-14 1.2632e-14 19 chr2 39536689 CAGGA 27 T GAGGC 0.88219 1e-14 1.2e-14 20 chr1 200594041 AACAA 8 T AAGGC 0.99484 1e-14 1.1429e-14 21 chr1 151196702 GATTG 9 T CCCCC 0.67961 1e-14 1.0909e-14 22 chr1 151196711 TTTTT 6 C TAGCA 0.0095938 3.0295e-05 3.1612e-05 23
but the output.prefix : Total_Number_of_Sites Number_of_Somatic_Sites % 24 23 95.83
the msi loci in output.prefix_germline means the stable loci? if that,the msi result will be: Total_Number_of_Sites Number_of_Somatic_Sites % 24 (23-15) 33.33
I'm very confused about this, and hope your reply!
I think the output.prefix_germline contained msi sites that had germline mutations, while the output.prefix_somatic included the msi sites that had somatic mutations. Total_Number_of_Sites refers to the total number of sites that passed quality control!
