BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237787.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 = 2,870,549 number of mapped reads = 2,522,220 (87.87%) number of supplementary alignments = 21,068 (0.73%) number of secondary alignments = 0 number of mapped bases = 160,972,739 bp number of sequenced bases = 160,872,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,179 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6589 >>>>>>> ACTG content number of A's = 42,684,928 bp (26.53%) number of C's = 29,985,596 bp (18.64%) number of T's = 50,434,043 bp (31.35%) number of G's = 37,728,462 bp (23.45%) number of N's = 39,112 bp (0.02%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,425,628 number of insertions = 13,133 mapped reads with insertion percentage = 0.52% number of deletions = 59,594 mapped reads with deletion percentage = 2.33% homopolymer indels = 44.89% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.5915X There is a 4.05% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 21963497 0.08811812348503638 1.254597914086572 chr2 243199373 3547207 0.014585592702165397 0.44992296149598876 chr3 198022430 7876334 0.039774958826633934 0.3130631182522984 chr4 191154276 6179589 0.03232775708349836 0.30392562233998227 chr5 180915260 13173845 0.07281776562131906 0.32965834139564165 chr6 171115067 7640431 0.04465083720535258 0.28907538135439037 chr7 159138663 7467840 0.04692662272775284 0.7088217117826464 chr8 146364022 12639888 0.08635925569194866 0.5024418911265434 chr9 141213431 6637933 0.047006385674461804 0.4103358455965979 chr10 135534747 9231799 0.06811389111900581 1.228317034904997 chr11 135006516 10484705 0.07766073305676593 0.4475200041822307 chr12 133851895 7378164 0.05512184941423504 0.2914324901921454 chr13 115169878 8139721 0.07067578034596858 0.3214649015464014 chr14 107349540 2204608 0.0205367251690133 0.2385538902024698 chr15 102531392 2748766 0.026809018646698955 0.19813635990909317 chr16 90354753 7057817 0.07811229366096546 0.45509796933872 chr17 81195210 5640646 0.06947018180013328 0.5775053776215444 chr18 78077248 4824774 0.06179487781126712 0.6656716662938899 chr19 59128983 4040717 0.06833733297932758 0.9600690891784968 chr20 63025520 3750564 0.05950865617610136 0.32082049259712697 chr21 48129895 3012337 0.06258764952634947 0.34863833864234206 chr22 51304566 1501668 0.02926967552946457 0.2074384718700072 chrMT 16571 143835 8.679922756623016 5.282471422167461 chrX 155270560 3210721 0.02067823417394772 0.22820697718852534 chrY 59373566 475333 0.008005801773806208 0.25073806820644406