samtools mpileup okuma atlama

aerijman

2019-08-22 05:51:18 UTC

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Şu komutu çalıştırıyorum:

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

ve şunu elde edin:

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

569930 pozisyonu ile ilgileniyorum.

Bamı şu şekilde inceliyorum:

  samtools myFile.bam chr1: 569929-569931

ve bakın:

  NS500355: NS500355: HHYN5BGXB: 2: 21311: 2303: 9255 99 CHR1 569.869 0 76 milyon = 569.900 107 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 GGCCTACTAACCAACACACACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCAC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE: ZEEE NM: i: 1 MD: Z: 1C74 XEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE: ZEEE NM: i: 1, MD: Z: 1C74 X: ZEE: Z76: 76M, NS500355: HHYN5BGXB: 1: 12105: 11868: 12011 99 CHR1 569.882 51 76m = 569.900 94 CTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACC / AAAAEEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEA NM: i: 0, MD: Z: 76 MC: Z: 76m: 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 CTAGGCATACTAACAACACACAACAATATACCAATGATACTAACAACACACAACAGATACCAATGATGATGATG // 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: 23110: 10125: 9334 CHR1 99 569.888 51 569.904 92 = 76m 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 // EEilinhwxtxltA // EE // A 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 'dir; 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: i: 76 XS: i: 71 RG: Z: ../ H2O Xa Z: chrM, -9342,76M, 1 'dir; NS500355: NS500355: HHYN5BGXB: 4: 11602: 21237: 3028 83 51 CHR1 76m = 569.900 569.900 -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 chr1 569901 51 76M = 569901 76 CCAACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACACCACC AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEE: 76,95: MCEE: ZEE: NM: 76, 1;
NS500355: NS500355: HHYN5BGXB: 2: 11203: 19.774: 18704 99 CHR1 569 904 11 76 milyon = 569 952 124 ACACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGT 6AAAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEE6EEEEAEEEAEEEEEEEEEEEEEEEEEEAE / E6EEAEEEEA NM: i: 0, MD: Z, 76 MC: Z: 76m AS 76 XS: i: 71 RG Z: H2O ../ XA kaynaktan: chrm, 9356,76M + 1; NS500355: NS500355: HHYN5BGXB: 2: 11309: 13954: 17.567 CHR1 569 905 99 11 76 milyon 569 972 = 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: 13252: 14049 CHR1 569 905 99 11 76 milyon 569 927 98 = CACACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTC AAAAAEE6EEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE6EEEEEEEEEEEEEEEEE / EEEE<EEEEEEEEEEE NM: i: 0, MD: Z, 76 MC: Z: 76m AS 76: XS ve 71 RG Z: H2O ../ XA: Z: chrM, + 9357,76 milyon, 1 ; NS500355: NS500355: HHYN5BGXB: 1: 22311: 21964: 12072 CHR1 83 569 908 52 569 908 -71 5S71M = GATCTACTAACCATATACCAATGATGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTG <AEEEA6EEE6EEEEEEEEEEEEEE / EEEEEEEEEEEEEEEEE / EEEEEEEEEEEEEEEEEEAAEEEAEEEAA6AA NM: i: 0, MD: Z, 71 MC: Z: 71M5S A.Ş. ve 71 XS : i: 66 RG Z: H2O ../ XA kaynaktan: chrm, -9360,5S71M 1; NS500355: NS500355: HHYN5BGXB: 4: 12602: 7858: 19.418 CHR1 99 569 909 15 569 917 84 76 milyon = 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: 12205: 19456: 7598 83 CHR1 569.927 0 76 milyon = 569.907 -96 TGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGA EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAA / EEEEEEEEEAAAAA NM: i: 1, MD: Z: 56G19 MC: Z: 76m: i: 71 XS: i: 76 RG: Z: ../ H2O XA: Z: chrM, -9379,76M, 0;

mapq ve konumlara göre (569930'a göre) cigar = 18S58M mpileup tarafından atlanır.

NEDEN? Yumuşak klips chr1: 569930 konumundan çok uzak