two insertions in one position

[maxineliu]

Hi,

I find two insertion records located in the same position when performing downstream analysis recently. There are 12 diploid samples in the VCF file. The ALT allele freq of Sniffles2.INS.317DM0 is 0.64 and the ALT allele freq of Sniffles2.INS.317EM0 is also 0.64. How does this happen? Sniffles version I used is 2.0.6.

Here are these two records:

NC_058080.1     19853140        Sniffles2.INS.317DM0    N       AGCACCTGCCCGCTTTAATAGGGCCCCTGCCCCCCTTAACCAGTGACCCCCACAACCCTGTCAAGAACCATGAACCAGAACGTACAACAAGAGATAAGTGGAAAAAGAAGAAGGTTTTTATTGAAGAGCAAGGCCTTAAGCAAAGTCCAAACGGATGGCTATACCGAAGCAGGTCTTGCGGAGACAGAGGTCAGGAACCAGAAGGGTAGGCAACTAGCAGGATCAGGAACTCAACGGGTAGTCAGACGAAGCCGGAATCAGGAACCAACGGGTAGTCCAGTCGTACCAGGATCAGGTGACCAACGGGAGTCAGACGAAGCCCAGAATCAGGAACCAACGGGGTAGTCAGACGAGGCCCAGGATCAGGAAACCAGAAGCAGCAGCAGGTCTTGGAAGCATGTGAACACAGGAGGACCAAGCAAGGAACTGAAACCACAGAACCTCCTAGAATATGAGCTGGCATCCACTCCTCCAGTGGGAAGGAGGAGCCGCAGGTGGGAGGCTAAAAAGAAAACCCAAACCAAGATGGCCGGCCAGCACATGTCAAAAGAAGGGAACAGCAAGGAAGGTAAGACCATGACAGTACCTCCCCCTCAAGGGCCCTCCTCCGCGGAGTAAGGAACGGTTTCTGAGGGAAGCCGTGCGTGAAGGGCTCGAGCAAGACAGAGACTGGACATCTATCTGCGAGGGAACCAGGAACGCTCCTCTGGACCAGAACCACGCCAATGGACCAAAAAACTGTAAACACCCGGCCGCGGACAGGCTGAGTCCAGGATATTTTCTCACTTCTCATACTCCTCACGATTGCCCACTCTGGACCGACGAGGCCGAGAATCGAGGAAGTGAAACGATTACACACCACGGCTTCAACAGGAGGACATGAACACGTTGGAGCTCCGCATGCCAGGAGGAAGCCGCAAGGGCATAGCTACCGGGTTTACCCTGCGAAGCAACTCGAAGGGACCAACAAAGAAGGCGCCAGCTTGGAGTGGCACTCTCGAAGGTTGAGGTTGCGGGTGGACTAACATACGCGGTCTCCGACCTGGTAGGAAGGACGGGCGCTCGTCTGCGCTCAGCCTGGGGGAATTTCGGCGCTGCGCAGAGACCTCAAGGACTCTGATCTGTACCCAAGAAGCTCGTAGGACGGAAAGGTGATCCTCCACAGCCGGAATATCCTGGGAGAGATATCTCCGGTAACACGGCAGGTTGAACCCATCATGGCCATGAAGGGAAACGTCCCAGAGGTAGAGTTCACCGCCGTGTTCCTTGCAAACTCAGCCCAACTGGGAAGGTCAACCCAATTGACGTGGTGATCGAGACATAGCAACGAAGGAAATTGCTCCAAGGCCTGATTGGACCGTTCTGCGGCCCCATTGGACCTGAGGGTGTAGGGGCCGAGGAAAATAAAGATAATCCCCACTGGAGCAAAAGGCGCGCCAGAACCTGGACACAAAACTGCTCCTCCCCCGATCCGACACATTCTCCTTGGGCAAACCGTGGCAACCAACGGAAGACCTCCCGTGGCAAAAATCGAGGCCAACTCTAGTGCAGGGCAGGGGGGTAACGTTCTATGTGAGAGGCAACACGAGTGTGTCACGGGTTTGGGGAATAGGCGCGCGTGCCAGGCTAGATCGATGAGAATGTTAGAGCACTATGGGGGGATTGCTCACTGGTTGGCATGAGAGGCAGGGGGGGGACACTAGAGTATCTCACAAGTACATCAAACTGACCACACTTGCCCCCACGGTTGTGACCATGACGCGCCCCGTCCGTTGGGTATGGCTGGCCCGGACTAGTCGATTGGGTTGCAAAAGGCCAACGGAAGTGCCAGGGACTTACTCTGGGCAAAACGGAGCATGCCGCTACATAGCGGGCGATGTCGGAACTAAGGGAAGGCCAACCAGAACAGAAGTGAAACAGCCCAGGACAGCGGATCTTTCCAGGAATGCCCGCGGCCTTGGAGTTATGGTAGGTTCGCAACAACCGATGTCGCACTCCTCAGGCACAAAACCACCTGCCGTTGGTCTTCTCCCAGAGGGAGCACCAGATTGAACCGCCAAAATCTGCTCACCCAGGGGAGAGGTCATGCTGGTGCGAATGGCGGCCAGGATCTGATTCGGAGGATGACCGAAGTCGAATCGACTCCACCCCGGACAGCTCGGAGTACTGCCGAGAATAAGGCATCCGCTCTGATGTTCTTGAAAACCGGGTAGTAGGAGACCACGTAATTAAACGTGACAAAACAGAGCCCATCTGGCTGACGTGGTGTCAATCTCTTGGCCTTAGAGAGGAAGGCAGATTCTTGTGGTCCGTCAGATGAGAACCGGAACCACCGAGCCCTCGAGCAAGTGCTCCATTCTTTAAGGGCCTGCACGATGGCCAATAACTCCCAGTCACCAATCATGATAGTTGCACTCCGCGAAGACAGTTTCCGGAGTAAAACCCACAAGGAAGCAGAGTACCCTCCGTGTTCTACGCTGAGACAGAGGGCGCCAACTCCCGTCTCAGACGCGTCCACCTCGAGACAAACGGCAACCCAGGTTTGGATGCGACAGAATCGTAGCCCGACCACAAATGCGGACTTTAGGCCTCAAAGCTTCGGATGGCCTCGGGCGGCAGACCTGGGGATTAACTTCCCTTCCTGTCAGATCCGTGAGAGGCTTGGCCTACATGGAAAAGTCCCTGAGAACTTCCGATAATAATTGGGCGAAGCCCAAAAAGCGCTGCAGGGCACGAAGACCATCTGGGCTGGGGCCACAGTAATACAGCCGAAACCTTCTCAGGATAAGGAGAACCCCTCACGGAAAATGATGTAACCCAAGAAGGTTACCTGGATCGTGAAAATTCACATTTCTCAAGCTTACCGAACAGTTGTTCTCTCGTAACCGTTGCAAACACTCGTCTGACATCCAGATGTGGGCCTCCATGGATTCAGAAATATACCAAGATGTCATCCAAATAGTCCACCACACACTGCTGCAACTGGTCAACGGAAAGCATCGATGATGAAAATTCCTGGAAACTGCGGGCGCAATGCACAACCCAAAGGCATAACCAAGGATTCAGAATGACGGTCACTGGTTGTTAAACGCGGTCTTCCACTCATCGCCCGCCTTGATCCTTACCATTATATGCCGCCCTCTAGTTGAGTTTGTAAAAGAACCGTGGCCCCGTTGAGGCAATCGAACAGCTCGGAAATCAAGGGTATGCGGGTAAGCTTCTTGATCTGATTGCGATTGAGACACCCCTTGTAATCGATGCAAGGCCTAAACTCACCGCCCTTCTTTTTCACACAGAAAACTTCCAGCCCCCTGCCGGGACGGGATTTGCGAATGGTCCGCGTGAAAAGCGGCCTCCTCACGTACTCCACATGGCCTCATTCTCCCGCTACCGACAGTGGATAGACTTTTGCCACAGAGAACGGCACCAGATTGTAACTCTATGGCACAATCATATGGGCGGTGCGGGAGGTAGGCAACCGCACGCACCGTATCGAATACATCCCGTACTCCTCGTAATTCAGGAGGCCAACAGAGCGTCCGAGGAAGTATCTCAGCAACTTACAGGCCCATGGATGCAACTAGCCCCAAACTGCGGTGACCCACGAGAGGATCTCGCCGATTTTTCCAATCGAAAGTCGGATTATGCTTCCTGGAGCCAGGGTACCCCAAGAACCACCGAGTAGTGTGGAGACGAAATAACCTGGAGACAGACCGACTCTCTGTGAGGCAACCAATGACCATCCCCACTGGAAGGGTCTCCTGATCACGTGTGGCGGCAGAAGGGTCTGCCGTCTATCGCCTCAAGAGCCAGCGGGGAACCTCGACTGCAGAGGAATGGAATTTGGCGTGCAGCGAACACACTATCAAGAACAAACCACCAGCACCAGAGCCACCAACGCCTGGTCAGTCACCAAGCCCCCGACCCAGGAGAGACAACATAATCAGTGGTTTTGTCAACACGGGAAACCGGGGACGAGGAGACACCACCCAAATCTGCCCCCGACAGACTCAGGTGCGGCGTTCTCCCGGACGGTTCGGACATGCCCAACCGAAAATGCCCAACCGTGACCCACGTACTGCAATCGGCCCCTCGCTCTCCGGAGTGCCCTCTCCCCCTCGACAGGCGAGCAAACCCCCCTCATGGGTTTTCACCCCCGACAAGTCATCCCAGGAGCGTGGAGGAGAGGGAGGCACGGGTGGGAACAGCAAACGTAGGCGCCAATCTGTTAGGATACCTCCGCAGGCTCTCCTAAAGGAAGGTCTCTCCCGGATCTGGTGGTCAATCAAAATCAGAAAGAAATCAGAGACTCGAGCTCCACTGGTAAGGTCCTTAGCAGCAACCCATCCTTCAAGGCATCCGAGAGACCATGAGAGAAGCAAGCGACCAGAGCCTCATTTATTCCGCCCACCTCTGCAGCCAGGGTACGTAACTCAATGGCGTATTCAGCTACGGAGCGTGAACCCTGTCTGATGGACTAAGGAGCTTCGCAGCAGAGGCAGCACGAGCCGGCACATCGAATACTTTTCTTCCGAAGAGAACAACAAACCGGAAACTCGCAAACCCCGGGGATTGTTGTTTCTCCCATAAAGGGCTGGCCCAGGCCAAGGCCTTGTCCAGAGCAACGAGATCAAGAATCCCACCTTTGATCTCTCAGTAGGAAAGGCATGTGCAGCAACTCGAAGTAAATGCCCACCTGGATAAGGCAACCTCGGCACTGAGTTTGGCTCTCCCCCAAAGCGCTGTGGAAGGGGGTCAGAACCGATCATACCCCGAGAAACACCACAGGCGCAGCAACAGTGTCGGGGTAGACCTCTGGCGCAACAACCGGAGCGGCAGTAGGACGGGCCCAGGAGCGACAACCAACCCCAACGGCAAACGGAAGCTAAATGAGCCCGTGCGTTACAAGCAGGGTTGCAACGCCACAGCGAACCGACCCAAACATGTTATCCTGCTGATCAAGTCTGGCAACCAGCGTATAGCGAGGTGGCCCTGTCCCGTCAGAATTCCATGGCTTGGTCCTAAAGTCAAGGAACCATGAACCAATGTACAACAAAGAAAAGTGGAAAAGAAAGAAGGTTTTATTGAAGAGCAAGCCGTAAGCAAAGTCAAACGGATTGTCTAAACCGAAGCAGGGTCTTGCGGAGACAGAGGTCAAGGAACCAAAGGGTAGTCAGACATAAAAAAAGGGAAAGGCCAGGATCAGGAACCAACGGGTAGTCAGACGAAGCCGGAATCAGGAACCAACGGGTAGTCAGACGTAGCCAGATCAGGAACCAACGGGTTAGTCAGACAAGCCGGAATCAGGAACCAACGGGGTAGTCAGACGAGCCAGGATCAGGAACCAGAAGCACAGCAGTCTTGGAAGCAATGTGAACACAGGCGGACCAAGCAAGGAACTGAAGCCCCCGCCACAGACCTCCTATTTAAATGAGCTGCCATCCACACCTCCAGTGGGAAGGAGAGCCGCAGGTGAGCTTACAAGAAACCCAGAAACCAGATGGCGCCAGCACATGTCAAACGAAGGGAACAGCAAGGAGGTAAACCATGAC57      PASS    IMPRECISE;SVTYPE=INS;SVLEN=5573;END=19853140;SUPPORT=4;COVERAGE=18,8,8,8,19;STRAND=+-;AC=14;STDEV_LEN=128.552;STDEV_POS=5.854;SUPP_VEC=010110110111;AN=22;AF=0.636364       GT:GQ:DR:DV:ID  0/0:0:39:0:NULL 0/1:38:22:10:Sniffles2.INS.54D3S0       0/0:0:15:0:NULL 0/1:0:7:2:Sniffles2.INS.4D44S0  1/1:33:0:12:Sniffles2.INS.53FCS0    0/0:0:20:0:NULL 1/1:52:0:19:Sniffles2.INS.50A3S0        1/1:13:0:5:Sniffles2.INS.4F97S0 ./.:0:3:0:NULL  1/1:19:0:7:Sniffles2.INS.52A8S0     1/1:33:0:12:Sniffles2.INS.4B5BS0        1/1:19:0:7:Sniffles2.INS.3F0AS0
NC_058080.1     19853140        Sniffles2.INS.317EM0    N       CTAGAAAATGGGGGGGGGGGGGGGGGAAAACAGCACCTGCCGCTTTAATAGTGGCCCCTGCCCCCATAACAGTGACCTCCCG      55 PASS     PRECISE;SVTYPE=INS;SVLEN=72;END=19853140;SUPPORT=6;COVERAGE=21,16,16,15,21;STRAND=+-;AC=24;STDEV_LEN=297.507;STDEV_POS=328.449;SUPP_VEC=111111111111;AN=22;AF=0.636364      GT:GQ:DR:DV:ID  1/1:60:3:36:Sniffles2.INS.5669S0,Sniffles2.INS.566AS0,Sniffles2.INS.566BS0      1/1:60:0:31:Sniffles2.INS.54D0S0,Sniffles2.INS.54D1S0,Sniffles2.INS.54D2S0  1/1:39:0:14:Sniffles2.INS.4AF5S0,Sniffles2.INS.4AF4S0,Sniffles2.INS.4AF6S0      1/1:27:0:10:Sniffles2.INS.4D41S0,Sniffles2.INS.4D42S0,Sniffles2.INS.4D43S0,Sniffles2.INS.4D45S0,Sniffles2.INS.4D46S0        1/1:41:0:15:Sniffles2.INS.53FAS0,Sniffles2.INS.53FBS0   1/1:55:0:20:Sniffles2.INS.4EAAS0,Sniffles2.INS.4EABS0,Sniffles2.INS.4EACS0,Sniffles2.INS.4EADS0     1/1:12:1:8:Sniffles2.INS.50A1S0,Sniffles2.INS.50A2S0    1/1:27:0:10:Sniffles2.INS.4F96S0    1/1:2:0:1:Sniffles2.INS.3D39S0,Sniffles2.INS.3D3BS0,Sniffles2.INS.3D3AS0        1/1:33:0:12:Sniffles2.INS.52A6S0,Sniffles2.INS.52A7S0       1/1:13:0:5:Sniffles2.INS.4B5AS0 1/1:33:0:12:Sniffles2.INS.3F09S0

Thanks, Maxine