BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524389.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 = 1,086,631 number of mapped reads = 995,595 (91.62%) number of supplementary alignments = 3,358 (0.31%) number of secondary alignments = 0 number of mapped bases = 57,623,676 bp number of sequenced bases = 57,605,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,626 duplication rate = 2.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6124 >>>>>>> ACTG content number of A's = 14,831,849 bp (25.75%) number of C's = 10,932,515 bp (18.98%) number of T's = 18,403,695 bp (31.95%) number of G's = 13,436,085 bp (23.32%) number of N's = 1,176 bp (0%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 285,753 number of insertions = 4,324 mapped reads with insertion percentage = 0.43% number of deletions = 11,425 mapped reads with deletion percentage = 1.14% homopolymer indels = 44.77% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.198X There is a 1.72% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4581019 0.01837916784969615 0.3188756194646124 chr2 243199373 4938191 0.020305114026753678 0.2672169756142444 chr3 198022430 3869739 0.019541922599374224 0.14897830281423272 chr4 191154276 3750826 0.019621983240385374 0.1565589041754273 chr5 180915260 3522608 0.019471038540364145 0.14815669107736423 chr6 171115067 3355510 0.019609670023972816 0.1606127725079065 chr7 159138663 3214594 0.020199956059703733 0.2739603557328584 chr8 146364022 2948420 0.020144431395852185 0.2129082717071439 chr9 141213431 2438960 0.017271444952003185 0.16689482150536877 chr10 135534747 2806879 0.02070966347839938 0.19866862051711517 chr11 135006516 2574691 0.019070864698115756 0.16717702053876218 chr12 133851895 2545793 0.019019476713422696 0.14801840647385653 chr13 115169878 1851370 0.01607512339294134 0.13524794083353714 chr14 107349540 1747191 0.016275719486082568 0.13718477000370163 chr15 102531392 1688887 0.016471901600633686 0.13864867966468336 chr16 90354753 1661710 0.018390952825691417 0.1538999186418251 chr17 81195210 1525079 0.018782869087967134 0.15103983684900632 chr18 78077248 1374291 0.017601683399496866 0.26589059557386524 chr19 59128983 1179387 0.01994600515960168 0.23532740790301246 chr20 63025520 1195301 0.018965349274389167 0.14690398914537955 chr21 48129895 751544 0.015614910441836617 0.13907425796026912 chr22 51304566 665812 0.012977636337475304 0.12137762332783518 chrMT 16571 2730 0.1647456399734476 0.4204630824201565 chrX 155270560 3246591 0.020909250278996868 0.1638795202782307 chrY 59373566 186553 0.0031420211479297033 0.09286195734886807