BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240219.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 = 2,601,901 number of mapped reads = 1,991,207 (76.53%) number of supplementary alignments = 20,714 (0.8%) number of secondary alignments = 0 number of mapped bases = 131,793,571 bp number of sequenced bases = 131,741,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 229,833 duplication rate = 8.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6421 >>>>>>> ACTG content number of A's = 37,484,279 bp (28.45%) number of C's = 24,343,570 bp (18.48%) number of T's = 41,859,424 bp (31.77%) number of G's = 28,042,128 bp (21.29%) number of N's = 12,414 bp (0.01%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,029,986 number of insertions = 9,707 mapped reads with insertion percentage = 0.48% number of deletions = 29,732 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.4552X There is a 2.29% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 9186851 0.03685788610332088 0.6202481870063551 chr2 243199373 10479480 0.04309007819687101 0.46898749953734364 chr3 198022430 12525181 0.06325132461004544 0.42679120520407443 chr4 191154276 10494308 0.05489967694994173 0.405483607755109 chr5 180915260 6517865 0.03602717095285384 0.3177396920806218 chr6 171115067 10014687 0.05852603850483838 0.44017092600750785 chr7 159138663 6394767 0.040183616472886916 0.4923393140677591 chr8 146364022 5670317 0.03874119419866721 0.7381002024178865 chr9 141213431 5629366 0.03986423925922457 0.4264958650010495 chr10 135534747 5824744 0.04297602001647592 0.4749690525612328 chr11 135006516 5531864 0.040974792653711616 0.48646249715313844 chr12 133851895 6399506 0.047810350387642996 0.3676225613063072 chr13 115169878 4450293 0.03864111933851315 0.3298221776181526 chr14 107349540 3881850 0.036160844284940576 0.3328812857712087 chr15 102531392 3882149 0.0378630283298992 0.3251028430642907 chr16 90354753 2925587 0.03237889433442422 0.317212422194704 chr17 81195210 2744694 0.03380364432827996 0.33267968427103006 chr18 78077248 3563984 0.04564689575124369 0.7257737244439358 chr19 59128983 2014303 0.03406625478405404 0.45186987104098886 chr20 63025520 2142610 0.033995911497437865 0.30377716116774767 chr21 48129895 2176330 0.04521784225791475 0.3691646107692235 chr22 51304566 1004438 0.019577945557516265 0.22121061549794663 chrMT 16571 28841 1.7404501840564843 2.487104885057989 chrX 155270560 7958342 0.05125467442121675 0.4053429859744615 chrY 59373566 351214 0.005915326022358165 0.1368681221438505