BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013330.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 = 1,361,804 number of mapped reads = 945,328 (69.42%) number of supplementary alignments = 2,201 (0.16%) number of secondary alignments = 0 number of mapped bases = 53,526,685 bp number of sequenced bases = 53,504,657 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,786 duplication rate = 6.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9967 >>>>>>> ACTG content number of A's = 13,917,054 bp (26.01%) number of C's = 7,716,590 bp (14.42%) number of T's = 18,065,132 bp (33.76%) number of G's = 13,789,329 bp (25.77%) number of N's = 16,552 bp (0.03%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 560,309 number of insertions = 2,970 mapped reads with insertion percentage = 0.31% number of deletions = 13,932 mapped reads with deletion percentage = 1.46% homopolymer indels = 51.18% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.1657X There is a 1.48% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 3904515 0.015665016136509446 0.17016110584483898 chr2 243199373 6691179 0.027513142478373085 0.2166216139453521 chr3 198022430 3297842 0.016653881078017272 0.1487015805208382 chr4 191154276 3203946 0.01676104802384855 0.15432584368396587 chr5 180915260 2378786 0.013148619967160316 0.1341510476400751 chr6 171115067 2683579 0.015682891325987092 0.1589989565838385 chr7 159138663 3543815 0.022268724225740166 0.23327298188092893 chr8 146364022 3103465 0.02120374226939459 0.19052056148003138 chr9 141213431 1926213 0.013640437643640285 0.1459945378825493 chr10 135534747 2334241 0.017222454401305667 0.1603002411017972 chr11 135006516 2357727 0.017463801524957506 0.1573851771827204 chr12 133851895 2817410 0.021048712085846823 0.1690624191040513 chr13 115169878 966753 0.008394147990675132 0.10452979115127307 chr14 107349540 1918756 0.01787390984628346 0.15679482115889815 chr15 102531392 1373925 0.01340004239872214 0.1400263645643629 chr16 90354753 1649238 0.018252919135311012 0.157536762934253 chr17 81195210 1399652 0.017238110474743523 0.1555671639338192 chr18 78077248 1033395 0.013235545904486798 0.1601301064827936 chr19 59128983 828252 0.01400754685735082 0.15111198012982618 chr20 63025520 1303780 0.02068654094404933 0.17053943582037012 chr21 48129895 1102410 0.02290489102459085 0.1803486512452192 chr22 51304566 424721 0.00827842496513858 0.10206942804895307 chrMT 16571 7705 0.46496892161004166 1.089546994463872 chrX 155270560 3172555 0.020432430977256732 0.17235981561541566 chrY 59373566 102825 0.0017318313001445794 0.04813620661157827