BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063579.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 = 2,118,158 number of mapped reads = 1,881,967 (88.85%) number of supplementary alignments = 9,012 (0.43%) number of secondary alignments = 0 number of mapped bases = 126,838,822 bp number of sequenced bases = 126,780,210 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,610 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.048 >>>>>>> ACTG content number of A's = 36,037,618 bp (28.43%) number of C's = 23,539,592 bp (18.57%) number of T's = 39,188,021 bp (30.91%) number of G's = 28,011,440 bp (22.09%) number of N's = 3,539 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,088,757 number of insertions = 9,589 mapped reads with insertion percentage = 0.51% number of deletions = 33,483 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.75% >>>>>>> Coverage mean coverageData = 0.041X std coverageData = 0.5327X There is a 3.6% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.04% 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 15687006 0.06293667769838776 1.2652382190068634 chr2 243199373 12716028 0.052286434143068286 0.3965396730099228 chr3 198022430 7065436 0.03567997827316835 0.232170336762531 chr4 191154276 7595569 0.039735281673740845 0.23404225731207037 chr5 180915260 6740419 0.03725732699386442 0.21430719565675702 chr6 171115067 7054571 0.04122705921624073 0.2574399446840255 chr7 159138663 9280138 0.05831479179889805 0.8489355918730543 chr8 146364022 5029381 0.03436213989801401 0.6369261429580514 chr9 141213431 4422143 0.031315314476000514 0.40814242609825807 chr10 135534747 7526550 0.05553225402781768 0.596669617204286 chr11 135006516 6898003 0.05109385238857656 0.3529316224589171 chr12 133851895 3666886 0.027395099636056703 0.19930890072338855 chr13 115169878 3810124 0.03308264336270288 0.19676201656963863 chr14 107349540 2547110 0.02372725584105903 0.22630001848880243 chr15 102531392 2052761 0.020020804945279587 0.1532055287442075 chr16 90354753 3219443 0.03563114161797332 0.2703774892121373 chr17 81195210 3114541 0.03835867904030299 0.24174699685563378 chr18 78077248 2765756 0.0354233284451829 0.7895552582229628 chr19 59128983 3168218 0.0535814728962952 0.8059120807430419 chr20 63025520 2132374 0.03383350109606394 0.22674585405243794 chr21 48129895 2096574 0.043560743276086514 0.2645969042417458 chr22 51304566 1425658 0.027788130982337907 0.1807593727041773 chrMT 16571 51680 3.1187013457244586 2.616872304200405 chrX 155270560 6469618 0.04166673965753714 0.26473482624128675 chrY 59373566 302835 0.005100502132548346 0.1764059834222204