BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,870,248 number of mapped reads = 1,431,835 (76.56%) number of supplementary alignments = 5,796 (0.31%) number of secondary alignments = 0 number of mapped bases = 86,860,338 bp number of sequenced bases = 86,812,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,648 duplication rate = 7.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3956 >>>>>>> ACTG content number of A's = 23,527,652 bp (27.1%) number of C's = 15,002,324 bp (17.28%) number of T's = 28,324,837 bp (32.63%) number of G's = 19,902,187 bp (22.93%) number of N's = 55,984 bp (0.06%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 879,386 number of insertions = 6,145 mapped reads with insertion percentage = 0.43% number of deletions = 27,972 mapped reads with deletion percentage = 1.93% homopolymer indels = 50.39% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.2891X There is a 2.11% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6555532 0.026300965565096826 0.4108628355072035 chr2 243199373 8914367 0.03665456407241642 0.3314497167727491 chr3 198022430 6358172 0.032108342474132856 0.23304173585409504 chr4 191154276 6201328 0.03244148197867151 0.24141270837814305 chr5 180915260 4617205 0.02552136840198002 0.2069622986801925 chr6 171115067 4688148 0.02739763413118963 0.24480297184184824 chr7 159138663 5332877 0.033510882267497745 0.4724217543606966 chr8 146364022 5076531 0.0346842819063827 0.4355909745660622 chr9 141213431 3532575 0.025015857025667766 0.25660697306748526 chr10 135534747 3488631 0.025739753658890144 0.2401333512791805 chr11 135006516 3941199 0.029192657634391512 0.2640940976299494 chr12 133851895 3959729 0.02958291326394744 0.2186579532505912 chr13 115169878 2126113 0.018460669030143456 0.17524851915200276 chr14 107349540 2965749 0.02762703035336714 0.21820530896562698 chr15 102531392 2294282 0.022376385956020182 0.20613713997122463 chr16 90354753 2306861 0.0255311527441174 0.20552900039946967 chr17 81195210 2360455 0.029071357780834608 0.23089152773018676 chr18 78077248 1958586 0.025085233536919743 0.3786523649639237 chr19 59128983 1560219 0.02638670446944775 0.30346852352452536 chr20 63025520 1661794 0.02636700181132976 0.21432032755052136 chr21 48129895 1266453 0.02631323006210589 0.2123696268536694 chr22 51304566 826522 0.016110106067362504 0.15727989105094242 chrMT 16571 62030 3.743286464305111 4.231780181652694 chrX 155270560 4605910 0.02966376884323725 0.23660482069829641 chrY 59373566 199070 0.003352838871089535 0.0764254080306468