BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008702.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 = 2,122,656 number of mapped reads = 1,103,137 (51.97%) number of supplementary alignments = 9,569 (0.45%) number of secondary alignments = 0 number of mapped bases = 72,291,840 bp number of sequenced bases = 72,253,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,139 duplication rate = 5.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7746 >>>>>>> ACTG content number of A's = 19,595,023 bp (27.12%) number of C's = 13,701,316 bp (18.96%) number of T's = 22,512,902 bp (31.16%) number of G's = 16,353,146 bp (22.63%) number of N's = 91,490 bp (0.13%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 630,764 number of insertions = 5,670 mapped reads with insertion percentage = 0.51% number of deletions = 21,152 mapped reads with deletion percentage = 1.9% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.0234X std coverageData = 0.3016X There is a 1.71% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7679165 0.030809010501923684 0.5556081629063631 chr2 243199373 3845917 0.01581384422401451 0.3002735226087516 chr3 198022430 8673157 0.04379886157340863 0.27983054911931343 chr4 191154276 2764105 0.014460074123583822 0.1703554041834653 chr5 180915260 5405825 0.029880425786083496 0.22545042901244305 chr6 171115067 2926186 0.01710069166498354 0.18607387740861542 chr7 159138663 2747236 0.017263158733462527 0.20012585666134233 chr8 146364022 2240308 0.015306411844845312 0.41745508923764096 chr9 141213431 2689071 0.01904260084155876 0.25240497908501386 chr10 135534747 5158778 0.03806240181346264 0.4907830317150851 chr11 135006516 1430421 0.010595199716138145 0.15805498064170034 chr12 133851895 3512181 0.02623930725821999 0.2269353157453502 chr13 115169878 1645606 0.014288510403735948 0.15270064624954993 chr14 107349540 2578181 0.024016693504229268 0.2375241053330905 chr15 102531392 2580368 0.025166614337977584 0.20467887948302893 chr16 90354753 2997718 0.03317720319594034 0.28572649512366505 chr17 81195210 3304270 0.04069538092210119 0.26945441082978155 chr18 78077248 1056151 0.013527000849210258 0.3892958765846973 chr19 59128983 1477234 0.0249832472173587 0.3800009829104427 chr20 63025520 1531696 0.024302790361745527 0.20774124529512433 chr21 48129895 1096449 0.022781038687077957 0.23510851503456237 chr22 51304566 971147 0.018929055944065486 0.17557215082168778 chrMT 16571 17469 1.0541910566652586 1.4239560827477038 chrX 155270560 3708269 0.023882627846515143 0.20984388698559195 chrY 59373566 254932 0.004293695278467863 0.17840408897173882