BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524343.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,732,561 number of mapped reads = 1,588,893 (91.71%) number of supplementary alignments = 6,252 (0.36%) number of secondary alignments = 0 number of mapped bases = 92,683,549 bp number of sequenced bases = 92,657,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,624 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6094 >>>>>>> ACTG content number of A's = 22,586,550 bp (24.38%) number of C's = 18,405,815 bp (19.86%) number of T's = 28,873,240 bp (31.16%) number of G's = 22,778,499 bp (24.58%) number of N's = 12,964 bp (0.01%) GC percentage = 44.45% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 479,227 number of insertions = 6,405 mapped reads with insertion percentage = 0.4% number of deletions = 16,734 mapped reads with deletion percentage = 1.05% homopolymer indels = 41.3% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.2962X There is a 2.67% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7832086 0.03142253354706787 0.5646039687817692 chr2 243199373 6099533 0.025080381272200074 0.3753570357015023 chr3 198022430 6394080 0.032289675467572033 0.1951668447395228 chr4 191154276 4869870 0.02547612379855944 0.22122518257366605 chr5 180915260 5470107 0.030235741307836607 0.19090115575184607 chr6 171115067 5878230 0.0343524980181903 0.2167690807315368 chr7 159138663 3708994 0.023306680665024816 0.3437898257189705 chr8 146364022 9681501 0.06614672695999022 0.38937800142851525 chr9 141213431 3897036 0.0275967800824838 0.2376419028028287 chr10 135534747 4699495 0.03467372835395487 0.30533785275323383 chr11 135006516 4444748 0.032922470201364205 0.24561641478078913 chr12 133851895 3681147 0.02750164276717935 0.18567810564291382 chr13 115169878 2357784 0.02047222799003052 0.1577957755994785 chr14 107349540 1969354 0.01834524861494516 0.15414912119950896 chr15 102531392 2892853 0.028214315085081456 0.18224748343402036 chr16 90354753 3000363 0.033206476697468255 0.2095114477880765 chr17 81195210 2917727 0.03593471831651153 0.22594610286550917 chr18 78077248 2163217 0.027706112285105132 0.39026666013241995 chr19 59128983 1694767 0.028662204455638954 0.36870419438877383 chr20 63025520 2216847 0.03517379943870356 0.20848252902046657 chr21 48129895 1366257 0.028386868494103303 0.22135179666566854 chr22 51304566 702174 0.013686384170952737 0.12809381149560234 chrMT 16571 14827 0.8947558988594533 1.1591492773648844 chrX 155270560 4422196 0.028480582539278536 0.20856520144643617 chrY 59373566 308356 0.005193489641501405 0.1874178675522533