BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063559.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 = 3,091,022 number of mapped reads = 2,781,475 (89.99%) number of supplementary alignments = 23,481 (0.76%) number of secondary alignments = 0 number of mapped bases = 181,645,324 bp number of sequenced bases = 181,565,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,122 duplication rate = 4.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8697 >>>>>>> ACTG content number of A's = 50,105,903 bp (27.6%) number of C's = 32,774,393 bp (18.05%) number of T's = 58,201,330 bp (32.06%) number of G's = 40,479,044 bp (22.29%) number of N's = 4,797 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,480,932 number of insertions = 13,762 mapped reads with insertion percentage = 0.49% number of deletions = 49,195 mapped reads with deletion percentage = 1.75% homopolymer indels = 46.32% >>>>>>> Coverage mean coverageData = 0.0587X std coverageData = 0.5549X There is a 4.68% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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% 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 19525700 0.07833761826414867 1.143726485512746 chr2 243199373 18867501 0.07758038504482494 0.7239223199360417 chr3 198022430 12387222 0.06255464090608322 0.3032543455662505 chr4 191154276 9784150 0.05118457303042491 0.28853019221249226 chr5 180915260 8907297 0.04923463614954316 0.26756145970715967 chr6 171115067 11696446 0.06835427297585665 0.3834815215226073 chr7 159138663 12791819 0.08038159149294852 0.80043864762897 chr8 146364022 6226593 0.042541827663085126 0.7798089452590636 chr9 141213431 5537162 0.03921129853434409 0.41761663479434846 chr10 135534747 8969736 0.06618034266888033 0.46203653259699373 chr11 135006516 7877141 0.058346376407491324 0.3933200331779254 chr12 133851895 7749675 0.05789738725775978 0.30386775359322266 chr13 115169878 5069773 0.04401995632920615 0.25734278156133744 chr14 107349540 4312784 0.0401751511930093 0.28182746374232276 chr15 102531392 2794722 0.027257232594676956 0.2149007835986263 chr16 90354753 3850579 0.04261623071450375 0.27487470129497976 chr17 81195210 4749446 0.05849416486514414 0.32286879886879666 chr18 78077248 5050695 0.06468843522763507 0.68911677441777 chr19 59128983 3828075 0.0647410932131202 0.770840165448441 chr20 63025520 2963938 0.04702758501635528 0.2780874450087257 chr21 48129895 3277170 0.0680901132238082 0.326657315982046 chr22 51304566 1476979 0.028788451304704536 0.19798358312523903 chrMT 16571 44924 2.7110011465813773 2.5846221600679287 chrX 155270560 13481004 0.08682266618990747 0.4112392183952638 chrY 59373566 424793 0.007154581215485693 0.1838150008439595