BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524496.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 = 7,066,607 number of mapped reads = 6,545,756 (92.63%) number of supplementary alignments = 15,763 (0.22%) number of secondary alignments = 0 number of mapped bases = 382,980,892 bp number of sequenced bases = 382,857,713 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 634,463 duplication rate = 6.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2347 >>>>>>> ACTG content number of A's = 92,049,307 bp (24.04%) number of C's = 68,221,335 bp (17.82%) number of T's = 125,127,245 bp (32.68%) number of G's = 97,452,123 bp (25.45%) number of N's = 7,703 bp (0%) GC percentage = 43.27% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,770,739 number of insertions = 24,364 mapped reads with insertion percentage = 0.37% number of deletions = 71,570 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.13% >>>>>>> Coverage mean coverageData = 0.1237X std coverageData = 0.9214X There is a 8.81% of reference with a coverageData >= 1X There is a 2.21% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 37654333 0.15107016724343486 1.8095003016290179 chr2 243199373 30067023 0.12363116988792566 1.0735901500539589 chr3 198022430 21074465 0.10642463583544551 0.45140380009169256 chr4 191154276 21368976 0.11178916029061259 0.6078524584036024 chr5 180915260 21002630 0.11609098093770531 0.4646670744212996 chr6 171115067 16531415 0.0966099320757067 0.6944284401068263 chr7 159138663 19096249 0.11999754578810305 1.3323426163210885 chr8 146364022 35305703 0.24121845326169022 0.8931327026534859 chr9 141213431 16292328 0.11537378480663076 0.7560796180929726 chr10 135534747 20084016 0.14818352079116656 0.9961726353356744 chr11 135006516 13014089 0.09639600654534333 0.9112921236786269 chr12 133851895 18013682 0.1345792078625409 0.5012910244851567 chr13 115169878 8511227 0.07390150226606995 0.37102998497180584 chr14 107349540 9128547 0.08503573466639913 0.419688853862825 chr15 102531392 10133140 0.09882963453768383 0.4777114089709557 chr16 90354753 11985434 0.13264862779271833 0.5840808628492272 chr17 81195210 13348199 0.164396384959162 0.6258341198740355 chr18 78077248 9008671 0.11538151293447228 1.5533494791870097 chr19 59128983 7756799 0.13118438042474026 1.268707260473742 chr20 63025520 10884455 0.1726991701139475 0.594895569703228 chr21 48129895 5250009 0.10908000110949753 0.5393589624248334 chr22 51304566 3113630 0.060689140221944375 0.32940670524267723 chrMT 16571 245116 14.791865306861384 9.17311520598603 chrX 155270560 22879808 0.14735445019326265 0.6681244034271525 chrY 59373566 1230948 0.02073225650620345 0.48729945119941526