BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716614.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 = 884,758 number of mapped reads = 803,111 (90.77%) number of supplementary alignments = 1,629 (0.18%) number of secondary alignments = 0 number of mapped bases = 46,757,960 bp number of sequenced bases = 46,744,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,705 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1655 >>>>>>> ACTG content number of A's = 11,905,595 bp (25.47%) number of C's = 9,465,748 bp (20.25%) number of T's = 14,321,962 bp (30.64%) number of G's = 11,050,579 bp (23.64%) number of N's = 516 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 218,239 number of insertions = 2,836 mapped reads with insertion percentage = 0.35% number of deletions = 8,691 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.28% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1616X There is a 1.41% of reference with a coverageData >= 1X There is a 0.07% 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 5309018 0.021299918847544216 0.20418628648692203 chr2 243199373 4651529 0.01912640210630806 0.20976570125575517 chr3 198022430 2925106 0.01477158925885315 0.12925208213219663 chr4 191154276 1942617 0.010162561050949235 0.10776973216265961 chr5 180915260 3314088 0.01831845472847343 0.1426599570935547 chr6 171115067 1737221 0.010152355549146353 0.11395322675048242 chr7 159138663 3069599 0.019288832406490684 0.2666903748064282 chr8 146364022 2027872 0.013854989582070928 0.1393658637566285 chr9 141213431 1251225 0.008860524038963404 0.13158354961614155 chr10 135534747 2635776 0.01944723444239727 0.1960139110697308 chr11 135006516 1893640 0.014026285960893918 0.15631547477195734 chr12 133851895 1810939 0.013529423696242776 0.12238848673227497 chr13 115169878 2170411 0.018845300852016186 0.14421925399717578 chr14 107349540 973039 0.009064212105613121 0.10443723771539876 chr15 102531392 1911944 0.018647401178363013 0.1445108520817793 chr16 90354753 1344818 0.014883754925432644 0.13743119046250307 chr17 81195210 1606230 0.019782324597719496 0.15407001367553452 chr18 78077248 1503838 0.019260899154642335 0.2577804868379135 chr19 59128983 684644 0.011578822520928527 0.1596780738213318 chr20 63025520 1128134 0.017899638114846177 0.1406737712686003 chr21 48129895 580759 0.012066492145889784 0.11713155886286607 chr22 51304566 474349 0.009245746275292534 0.10086002685056494 chrMT 16571 12153 0.7333896566290508 0.9582618548860979 chrX 155270560 1704366 0.010976749230504483 0.12710708484111874 chrY 59373566 94645 0.0015940595516866884 0.04722131657403142