Jeg kjører kommandoen:

  samtools mpileup -O -s -q20-B -Q20 -f hg19.fa -r chr1: 569929-569931 myFile.bam  

og få:

  chr1 569929 G 7 ... ,,., EEEEEEE NTTVTTU 53,48,42,60,30,29,27chr1 569930 C 6 .. .,., EEAEEE NTTTTU 54,49,43,31,30,28chr1 569931 G 6 ...,., EEEEEE NTTTTU 55,50,44,32,31,29  

Jeg er interessert i posisjon 569930 .

Jeg inspiserer bam med:

  samtools view myFile.bam chr1: 569929-569931  

og jeg ser:

  NS500355: NS500355: HHYN5BGXB: 2: 21 311: 2303: 9255 99 chr1 569869 0 76M = 569900 107 CTCCATAACGCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEAEEEEEEE NM: i: 2 MD: Z: 5C3C66 MC: Z: 76M AS: i: 66 XS: i: 71 RG: Z: ../ H2O XA: Z: chrM, + 9321,76M, 1; NS500355: NS500355: HHYN5BGXB: 4: 22603 : 25857: 2799 99 chr1 569877 45 76M = 569896 95 CGCTCCTCATACTA GGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NM: i: 1 MD: Z: 1C74 MC: Z: 74: 7: 6: NS500355: HHYN5BGXB: 1: 12105: 11868: 12011 99 chr1 569882 51 76M = 569900 94 CTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACC / AAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEA NM: i: 0 MD: Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z : ../ H2O XA: Z: chrM, + 9334,76M, 1; NS500355: NS500355: HHYN5BGXB: 2: 13301: 2681: 6114 99 chr1 569888 9 76M = 569952 140 CTAGGCATACTAACCAACACACACACACATATACCAAGACAGACAGACA // EEAEEE / E / EEEE ///// A / EE / EE / EE / E // EE / EEEE / E / AEA #### NM: i: 4 MD: Z: 6C19C15C29G3 MC: Z: 76M AS : i: 57 XS: i: 52 RG: Z: ../ H2O XA: Z: chrM, + 9340,76M, 5;
NS500355: NS500355: HHYN5BGXB: 2: 23 110: 10 125: 9334 99 569888 51 chr1 76M = 569904 92 CTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCC AAA / AEE6EEEE6E /// E / A / AAE / E / AEEEEEEE / EE / EEEAEEEEAEE // EEEEEEAEEEAEEAE / AEE / AEE< NM: i: 0 MD: Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: chrM, + 9340,76M, 1; NS500355: NS500355: HHYN5BGXB: 1: 13209: 10692: 11045 83 chr1 569888 53 18S58M = 569888-58 CGTGTGCTCTTCCGATCTCTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAG EE<A / EE // E //E // E //E // E //E //E / / EE A / E / E // AEAEEEEE6A6AAA NM: i: 0 MD: Z: 58 MC: Z: 59M17S AS: i: 58 XS: i: 53 RG: Z: ../ H2O XA: Z: chrM, -9340, 18S58M, 1; NS500355: NS500355: HHYN5BGXB: 1: 21304: 26480: 15673 569 890 11 83 chr1 76M = 569 796 -170 AGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCAC AEEEEEEEAAEEEEEEEEEEEE / EEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA NM: i: 0 MD: Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: CHRM -9342,76M, 1; NS500355: NS500355: HHYN5BGXB: 4: 11 602: 21 237: 3028 83 569900 51 chr1 76M = 569900 -76 ACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCAC EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAA NM: i: 0 MD: Z: 76 MC: Z : 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: chrM, -9352,76M, 1; NS500355: NS500355: HHYN5BGXB: 3: 13504: 4369: 8812 99 chr 569901 51 76M = 569901 76 CCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE NM: i: 0 MD: Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: CHRM + 9353,76M, 1;
NS500355: NS500355: HHYN5BGXB: 2: 11203: 19774: 18704 99 chr1 569904 11 76M = 569952 124 ACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGT 6AAAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE6EEEEAEEEAEEEEEEEEEEEEEEEEEEAE / E6EEAEEEEA NM: i: 0 MD: Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: CHRM + 9356,76M, 1; NS500355: NS500355: HHYN5BGXB: 2: 11 309: 13 954: 17 567 569 905 11 99 chr1 76M = 569972 143 CACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE NM: i: 0 MD : Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: chrM, + 9357.76M, 1; NS500355: NS500355: HHYN5BGXB: 1: 21202: 13 252: 14 049 569 905 11 99 chr1 76M = 569927 98 CACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTC AAAAAEE6EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEE / EEEE<EEEEEEEEEEE NM: i: 0 MD: Z: 76 MC: Z: 76M AS: i: 76 XS: i: 71 RG: Z: ../ H2O XA: Z: chrM, + 9357,76M, 1 ; NS500355: NS500355: HHYN5BGXB: 1: 22311: 21964: 12072 569 908 52 83 chr1 5S71M = 569908 -71 GATCTACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTG <AEEEA6EEE6EEEEEEEEEEEEEE / EEEEEEEEEEEEEEEEE / EEEEEEEEEEEEEEEEEEAAEEEAEEEAA6AA NM: i: 0 MD: Z: 71 MC: Z: 71M5S AS: i: 71 XS : i: 66 RG: Z: ../ H2O XA: Z: CHRM -9360,5S71M, 1; NS500355: NS500355: HHYN5BGXB: 4: 12 602: 7858: 19 418 569 909 15 99 chr1 76M = 569917 84 CTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE / AAEEEEEEEEEEEEEEE NM: i: 1 MD: Z: 74G1 MC: Z: 76M AS: i: 74 XS: i: 71 RG: Z: ../ H2O XA: Z: chrM, + 9361.76M, 1;
NS500355: NS500355: HHYN5BGXB: 2: 12 205: 19 456: 7598 83 chr1 569927 0 76M = 569907 -96 TGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGA EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA / EEEEEEEEEAAAAA NM: i: 1 MD: Z: 56G19 MC: Z: 76M AS: i: 71 XS: i: 76 RG: Z: ../ H2O XA: Z: chrM, -9379,76M, 0;  

Basert på mapq og posisjoner (respekt for 569930) Jeg ser at avlesningen med sigar = 18S58M hoppes over av mpileup.

HVORFOR? Det myke klippet er langt fra posisjon chr1: 569930