BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524563.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 = 2,047,034 number of mapped reads = 1,882,648 (91.97%) number of supplementary alignments = 7,604 (0.37%) number of secondary alignments = 0 number of mapped bases = 110,071,839 bp number of sequenced bases = 110,037,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,031 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0374 >>>>>>> ACTG content number of A's = 28,036,771 bp (25.48%) number of C's = 22,698,376 bp (20.63%) number of T's = 33,237,247 bp (30.21%) number of G's = 26,063,961 bp (23.69%) number of N's = 1,536 bp (0%) GC percentage = 44.31% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 557,772 number of insertions = 7,596 mapped reads with insertion percentage = 0.4% number of deletions = 20,682 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.18% >>>>>>> Coverage mean coverageData = 0.0356X std coverageData = 0.3182X There is a 3.09% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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 9903739 0.03973405947903336 0.5865402119086311 chr2 243199373 8869421 0.03646975274068655 0.3574161233047467 chr3 198022430 6037290 0.030487909879704032 0.19555017505650285 chr4 191154276 6043695 0.03161684439640785 0.2348284638424555 chr5 180915260 6215568 0.03435623949024532 0.2076985100709631 chr6 171115067 4642080 0.027128411783867053 0.235004895936265 chr7 159138663 5616002 0.03528999109411897 0.4050540409455624 chr8 146364022 9967242 0.06809898951806613 0.3543722994842335 chr9 141213431 4795757 0.033961054313594294 0.2748468292300611 chr10 135534747 5653075 0.041709414929589975 0.32952178228361534 chr11 135006516 3841121 0.028451374895119876 0.28999340023722686 chr12 133851895 5266518 0.03934586058718108 0.2257527907565624 chr13 115169878 2543389 0.022083803891847484 0.16706006027634956 chr14 107349540 2622532 0.024429839196330044 0.17893680272860266 chr15 102531392 2985552 0.029118418679032466 0.19536345281767645 chr16 90354753 3518885 0.038945211880552645 0.23830265480198787 chr17 81195210 4060916 0.050014231135063265 0.26689610155794896 chr18 78077248 2579293 0.033035142324688495 0.516159231439828 chr19 59128983 2339490 0.03956587584129428 0.41954845379330297 chr20 63025520 3233388 0.05130283732684792 0.25845681079769406 chr21 48129895 1519238 0.03156537116900006 0.22729474665869479 chr22 51304566 948315 0.018484027328093955 0.15135846669428737 chrMT 16571 4920 0.2969042302818176 0.5699421436945462 chrX 155270560 6494869 0.041829365463742774 0.2543659230316247 chrY 59373566 369544 0.006224049267985689 0.19824163932616679