which indel to consider

Question

[Kritika]

Hi All, First of all sorry if this question is silly or already answered please bear I have bam file

FHVOG:09133:14031       0       chr1    14716   4       201M    *       0       0       CGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGA
FHVOG:09370:07492       0       chr1    14716   3       100M1I22M1D38M1I7M1I25M1I8M     *       0       0       CGTCCTCCTCTGCCTGTGGCTGCTGCGGTGG
FHVOG:10241:08743       0       chr1    14716   5       201M    *       0       0       CGTCCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGA
FHVOG:03597:12789       16      chr1    14719   3       198M    *       0       0       CCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACAC
FHVOG:05122:10044       16      chr1    14719   3       198M    *       0       0       CCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACAC
FHVOG:06178:07535       16      chr1    14719   0       165M1D32M       *       0       0       CCTCCTCTGCCTGTGGCTGCTGCGGTGGCGGCAAAGGAGGGATGGAG

My doubt is how will i get know which is true mapped i mean which cigar value and mapping quality to be considered In above bam file at chr1 position 14716 there are many cigar value with different mapping quality I know samtools does filtering using given threshold for quality filter But i came across region in bam file which look like this :-

FHVOG:07330:07541       0       chr1    14724   2       37M1I25M1I4M1I56M1I9M1I17M1I37M1I8M     *       0       0       CCTGCCTGTGGCTGCTGCGGTGG
FHVOG:01692:01183       16      chr1    14724   0       28M1I17M1I11M1D11M1I64M1D20M1D38M2S     *       0       0       GCTGCCTGTGGCTGCTGCGGTGG
FHVOG:02541:12172       16      chr1    14724   1       15M1I13M1D21M1I42M1I29M1I32M1D40M       *       0       0       TCTGCCTGTGGCTGCTTGCGGTG
FHVOG:02930:05800       16      chr1    14724   3       28M1I165M       *       0       0       GCTGCCTGTGGCTGCTGCGGTGGCGGCAGGAGGAGGGATGGAGTCTG
FHVOG:03247:00710       16      chr1    14724   1       13M1I14M1D6M2I18M1D5M2D133M     *       0       0       GCTGCCTGTGGCTGGCTGCGGTGGCGGCGAG
FHVOG:03337:05066       16      chr1    14724   3       13M1I15M1I114M1D50M     *       0       0       GCTGCCTGTGGCTGGCTGCGGTGGCGGCAGGAGGAGGGA
FHVOG:03375:12099       16      chr1    14724   2       29M2I156M1D7M   *       0       0       GCTGCCTGTGGCTGCTGCGGTGGCGGCAGGAGGGAGGGATGGAGTCT
FHVOG:03908:01407       16      chr1    14724   0       13M1I3M1I11M2I166M      *       0       0       GCTGCCTGTGGCTGGCTGGCGGTGGCGGCGAGGAGGAGG
FHVOG:04263:05716       16      chr1    14724   3       160M1D32M       *       0       0       GCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGA
FHVOG:05542:03460       16      chr1    14724   4       193M    *       0       0       GCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGG
FHVOG:06028:07753       16      chr1    14724   4       193M    *       0       0       GCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGG
FHVOG:07525:03306       16      chr1    14724   4       193M    *       0       0       GCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATGGAGTCTGACACGCGGG

Now for such type of reads if i give threshold in samtools to filter out reads having mapping quality less then 3 it will eliminate all reads below 3 but again i am getting several cigar value with map Q 3 so which is true to consider for downstream analysis specially for indel calls

Thanks

[Brian Bushnell]

I suggest you look at the regions in IGV, which makes it more clear what's going on, and also use a variant caller to get its opinion what what the truth is. The data you have posted is not sufficient to see how well the reads match the reference because they are using legacy cigar strings with "M" symbols instead o "=" and "X" so it's not clear where there are matches or mismatches. But since you're aligning to a fairly low-complexity region it's more likely that it's misassembled, or that the mapping is incorrect. You might want to post a screenshot of IGV here.

[Kritika]

FHVOG:07330:07541 0 chr1 14724 2 37M1I25M1I4M1I56M1I9M1I17M1I37M1I8M * 0 0 CCTGCCTGTGGCTGCTGCGGTGGCGGCAGAGGAGGGATTGGAGTCTGACACGCGGGCAAAGGCTTCCTCCCGGGCCCCTCACCAGCCCCAGGCCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTCGAGTGAGGGTTGGTTGGTGGGAAACCCTTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAAGGC 715=<6:6//)/798=:==7//*/949>=>=8<<<488177<:9:<<777<<<<=7==<6;8::386777)6;4;;>8==8=>9==;:---636506661666.5,2---655115?,.,.3:3:..-;19928=-6.426+4444&5:::::+979:<9:6:?6887--+-5:;==<<'-)3 MD:Z:0T88T103 RG:Z:1 NM:i:9 AS:i:142 XS:i:137 FHVOG:01692:01183 16 chr1 14724 0 28M1I17M1I11M1D11M1I64M1D20M1D38M2S * 0 0 GCTGCCTGTGGCTGCTGCGGTGGCGGCAGGAGGAGGGATGGAGTCTGGACACGCGGGCAAGGCTCCTCCGGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGTTGGTGGGAAACCCTGGTTCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGGC 4444-4.66044,-,,--18,)..18877<84882888<6955555/558:55/197/)/)///3997:/:::/::9::50777/<<<<8<=8>8<=7=<<;;;;<<7;;6<<4;7)7770;778<:87/)///0)/)9/*55*87*=;84848-88885'88880=899@<>7?===;;7:6:5'5555785 MD:Z:0T55^A75^G20^C38 RG:Z:1 NM:i:7 AS:i:146 XS:i:146 FHVOG:02541:12172 16 chr1 14724 1 15M1I13M1D21M1I42M1I29M1I32M1D40M * 0 0 TCTGCCTGTGGCTGCTTGCGGTGGCGGCAAGGAGGGATGGAGTCTGACACGGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTTCCCAGAGATGCCTGGAGGGAAAAGGCTTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCAGCCCCGGAAGACTTAAATACAGGAAGAAAAAGGCA ,,,,0667:498/////948/,//38/)/)//)88/53555==8888884883;;;4::69885::682881<<>>=;7=;;2BB>=6:94/(///)////667850554::3;5(444/57/77;98:;4;;;9<7<7;5/55/::3:55/5/5)55555)555080;:;709+=<:;:945/5/'////)//) MD:Z:28^G124^C10C1G27 RG:Z:1 NM:i:8 AS:i:140 XS:i:135 FHVOG:02930:05800 16 chr1 14724 3 28M1I165M * 0 0 GCTGCCTGTGGCTGCTGCGGTGGCGGCAGGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGC ::9;6:677366,,,**-),,477048/)//)//5<<<<9;<<<<<<<=<<<<7C<;4;;3=6>?5>?>==<8<<7/77784::68*992@<<<=<8876::399/9:08883:;<=<<<=929997=892985;;4;<6>==8>78(88889;-<<<<4=;<<9292A?===;6;5<;-;<;;5@> MD:Z:0T192 RG:Z:1 NM:i:2 AS:i:185 XS:i:180 FHVOG:03247:00710 16 chr1 14724 1 13M1I14M1D6M2I18M1D5M2D133M * 0 0 GCTGCCTGTGGCTGGCTGCGGTGGCGGCGAGGAGGAGGATGGAGTCTGACACGCGGCAAGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGC ::;9444/8396/)/////-44-44-7665/5/37/)//6366444,-,,--6-)//)///=7A=9=8=>7>?><<;5<;=1<><<9@?9=7<<6=<<=<<<<;6<<8885>=7@?<7;;::::455+9994;4=9=<6A;6;<6;;;5;57'85875=-=<<=9A<<<=9<7@<=>?<9<8<8)88880>; MD:Z:0T26^A24^G5^AG133 RG:Z:1 NM:i:8 AS:i:151 XS:i:146 FHVOG:03337:05066 16 chr1 14724 3 13M1I15M1I114M1D50M * 0 0 GCTGCCTGTGGCTGGCTGCGGTGGCGGCAGGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGC 6686/77;<6<<94:97880777<<6::/)//5881;:;7175:99575:;::7*777*88088?7<;78*99*><<=@>9===7>>>=8==8;4;;6?><<<<=<<8==9<<6<<2=<:5;;<<<<;;8+855/:3949919/)/)77/)/)/'////55'77770:788=8;3;;;;::8:6;;-;;;;5<= MD:Z:0T141^A50 RG:Z:1 NM:i:4 AS:i:170 XS:i:165 FHVOG:03375:12099 16 chr1 14724 2 29M2I156M1D7M * 0 0 GCTGCCTGTGGCTGCTGCGGTGGCGGCAGGAGGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCAGCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAAGGCTGAGTGAGGGTGGTTGGTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAGGC 44::5:8:7377/////5-89299476/)//)///*5555/55;:;888<<<<<9BB>8@@@<<<9==9=8>=4<=;<;;5<<<3>=;;6=<7:0:7*888<;;<883==9>=7??5??<7<;<<<<:;<8A<=9=8;6<:4<<5;;4?;95:45'555558'88880<;;=>9>8=>;;::594;8)8880;: MD:Z:0T28A155^A7 RG:Z:1 NM:i:5 AS:i:175 XS:i:170

IGV screen shot for chr1 position 14724 https://ibb.co/hbr8dQ