BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714130.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 742,628 number of mapped reads = 456,185 (61.43%) number of supplementary alignments = 14,890 (2.01%) number of secondary alignments = 0 number of mapped bases = 58,571,099 bp number of sequenced bases = 57,428,391 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,763 duplication rate = 43.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.4749 >>>>>>> ACTG content number of A's = 16,066,690 bp (27.98%) number of C's = 12,024,371 bp (20.94%) number of T's = 15,244,829 bp (26.55%) number of G's = 14,092,130 bp (24.54%) number of N's = 371 bp (0%) GC percentage = 45.48% >>>>>>> Mismatches and indels general error rate = 0.0427 number of mismatches = 2,250,363 number of insertions = 64,169 mapped reads with insertion percentage = 13.43% number of deletions = 195,538 mapped reads with deletion percentage = 40.88% homopolymer indels = 28.9% >>>>>>> Coverage mean coverageData = 0.0189X std coverageData = 2.6994X There is a 0.06% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4783977 0.019193440645429726 2.114430183965368 chr2 243199373 6614763 0.027198931141981193 6.717241528961769 chr3 198022430 2914753 0.014719307302713132 1.3485566633208235 chr4 191154276 3030997 0.015856286678096597 1.7094737144754788 chr5 180915260 2850884 0.0157581179166423 1.4141489233110398 chr6 171115067 2427392 0.014185729185379099 1.4604358306003837 chr7 159138663 2315501 0.014550210215100274 1.5086058486639446 chr8 146364022 3117072 0.021296709105192532 2.829428370175807 chr9 141213431 2238602 0.015852613906109255 1.8586228276488406 chr10 135534747 3381761 0.024951247372749365 2.3574725899882196 chr11 135006516 2964108 0.02195529584660936 2.1223489679227874 chr12 133851895 2514509 0.01878575570409369 2.0926979460777537 chr13 115169878 1637550 0.014218561558257447 1.5244072326943603 chr14 107349540 1943916 0.018108284395070534 1.8243367330105442 chr15 102531392 1461100 0.01425026981004998 1.5273735718039188 chr16 90354753 2157815 0.02388158816614772 2.598831973991256 chr17 81195210 1816793 0.022375617970567474 2.5624207011138473 chr18 78077248 1420354 0.018191650402432216 1.8694686080182077 chr19 59128983 1340197 0.02266565281530379 2.416061448930007 chr20 63025520 1588705 0.025207328713828938 2.134371744121001 chr21 48129895 544874 0.01132090564502582 1.0357476134973806 chr22 51304566 591144 0.01152224930623134 1.459713944763495 chrMT 16571 493542 29.78347715889204 274.7543208435765 chrX 155270560 4115442 0.02650497299681279 1.752461348326082 chrY 59373566 305348 0.005142827365295862 0.8088830962372984