BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524415.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 = 1,284,364 number of mapped reads = 1,179,842 (91.86%) number of supplementary alignments = 4,468 (0.35%) number of secondary alignments = 0 number of mapped bases = 68,923,000 bp number of sequenced bases = 68,903,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,376 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7629 >>>>>>> ACTG content number of A's = 17,354,479 bp (25.19%) number of C's = 12,722,761 bp (18.46%) number of T's = 22,196,813 bp (32.21%) number of G's = 16,620,706 bp (24.12%) number of N's = 8,393 bp (0.01%) GC percentage = 42.59% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 335,007 number of insertions = 4,552 mapped reads with insertion percentage = 0.38% number of deletions = 12,620 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.0223X std coverageData = 0.2392X There is a 2.04% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5747164 0.023057772040616098 0.49507985890154055 chr2 243199373 5676702 0.023341762480612975 0.2524676655196973 chr3 198022430 4846658 0.024475298076081585 0.16655417554800303 chr4 191154276 4647675 0.024313738082427202 0.1778663055977672 chr5 180915260 4294205 0.02373600214818805 0.16397702963204708 chr6 171115067 2787685 0.01629128894885685 0.14500000850457617 chr7 159138663 3878535 0.024372047162417095 0.32584128678722146 chr8 146364022 3644916 0.02490308718081005 0.2328802989128363 chr9 141213431 2567125 0.018179042756917365 0.1782524209729117 chr10 135534747 3375201 0.024902846500314785 0.21399319055232482 chr11 135006516 2867979 0.021243263547368336 0.18827009640458628 chr12 133851895 3204928 0.023943837328563783 0.16861299635051344 chr13 115169878 2218773 0.01926521967836069 0.14798333973116792 chr14 107349540 1940169 0.018073379727570327 0.14804963180770964 chr15 102531392 2102537 0.020506275775520534 0.15274743434300442 chr16 90354753 2049594 0.022683853720456743 0.16587084163702961 chr17 81195210 1792102 0.022071523677320373 0.17028606975232766 chr18 78077248 1908451 0.024443113056443793 0.29014288550365974 chr19 59128983 1837252 0.031071936413991766 0.3531777361956123 chr20 63025520 1852368 0.02939076107583087 0.1886819236928796 chr21 48129895 954121 0.019823874537852202 0.16444460329120866 chr22 51304566 464262 0.009049136094436507 0.10025247054027261 chrMT 16571 48505 2.927101562971456 2.647715957224776 chrX 155270560 4010208 0.02582722700298112 0.18703589352173042 chrY 59373566 205885 0.003467620590617717 0.1010087805627129