BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237305.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,073,811 number of mapped reads = 2,749,970 (89.46%) number of supplementary alignments = 31,223 (1.02%) number of secondary alignments = 0 number of mapped bases = 172,313,813 bp number of sequenced bases = 172,237,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,006,735 duplication rate = 20.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9394 >>>>>>> ACTG content number of A's = 43,547,679 bp (25.28%) number of C's = 31,143,141 bp (18.08%) number of T's = 55,908,330 bp (32.46%) number of G's = 41,619,264 bp (24.16%) number of N's = 18,632 bp (0.01%) GC percentage = 42.25% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 984,622 number of insertions = 13,436 mapped reads with insertion percentage = 0.48% number of deletions = 43,140 mapped reads with deletion percentage = 1.55% homopolymer indels = 42.05% >>>>>>> Coverage mean coverageData = 0.0557X std coverageData = 0.8128X There is a 1.68% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.55% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 23988080 0.09624080334788815 0.9020326097650971 chr2 243199373 14500684 0.059624676746185525 1.5865359808976705 chr3 198022430 11389857 0.05751801449967057 0.5931101185149918 chr4 191154276 7459482 0.03902335933097306 0.6565546732941226 chr5 180915260 6998010 0.038681148290088965 0.4782442227276268 chr6 171115067 18611787 0.10876766918485326 1.001189856017701 chr7 159138663 11256505 0.07073394226015334 0.7239769660049366 chr8 146364022 6340329 0.0433189038765278 0.6476943036405042 chr9 141213431 8018160 0.0567804347165816 0.6714421231984957 chr10 135534747 11236782 0.08290702014591136 0.9817304804995187 chr11 135006516 5367264 0.03975559224119227 0.5176201413297706 chr12 133851895 3192713 0.02385257974868417 0.4003566547406429 chr13 115169878 3839109 0.03333431507151549 0.48865981678151005 chr14 107349540 6602368 0.061503458701360064 0.6378013539841452 chr15 102531392 2709447 0.02642553609337519 0.42248405274811895 chr16 90354753 3137008 0.03471879337659193 0.5075307672746792 chr17 81195210 5404099 0.0665568695493244 0.6478128901097538 chr18 78077248 4305960 0.055149997090061374 1.5364251375623732 chr19 59128983 1609629 0.027222335280145102 0.5637180196319671 chr20 63025520 6518700 0.10342953140251758 0.8252808711983405 chr21 48129895 2223022 0.04618796695899711 0.5944400219725448 chr22 51304566 865720 0.016874131631870737 0.29923995187063707 chrMT 16571 11583 0.6989922153159134 1.9447154332836283 chrX 155270560 6100024 0.03928641720619801 0.4947269585481659 chrY 59373566 627491 0.010568524720243349 0.4895870430157393