BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716941.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 = 591,590 number of mapped reads = 449,523 (75.99%) number of supplementary alignments = 593 (0.1%) number of secondary alignments = 0 number of mapped bases = 23,578,551 bp number of sequenced bases = 23,572,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,871 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.411 >>>>>>> ACTG content number of A's = 5,035,285 bp (21.36%) number of C's = 4,344,053 bp (18.43%) number of T's = 7,649,274 bp (32.45%) number of G's = 6,543,472 bp (27.76%) number of N's = 453 bp (0%) GC percentage = 46.19% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 156,967 number of insertions = 1,252 mapped reads with insertion percentage = 0.28% number of deletions = 3,532 mapped reads with deletion percentage = 0.78% homopolymer indels = 39.32% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 0.1015X There is a 0.7% of reference with a coverageData >= 1X There is a 0.05% 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 2192259 0.008795400353285378 0.11515917940153035 chr2 243199373 1945573 0.007999909605030109 0.13423349332314047 chr3 198022430 1512846 0.007639770908780384 0.09348957612584366 chr4 191154276 1450906 0.007590235648194446 0.09629307079755448 chr5 180915260 2012227 0.01112248353179273 0.11273887942134586 chr6 171115067 926133 0.005412340457430321 0.08671475321000592 chr7 159138663 1314447 0.00825975897510211 0.10702077699449201 chr8 146364022 1393645 0.00952177304884393 0.10688383306288063 chr9 141213431 979541 0.0069365993947133825 0.09247609177492498 chr10 135534747 1179778 0.008704616536451718 0.10939990070484137 chr11 135006516 957295 0.007090731828084505 0.09745812931918764 chr12 133851895 1088002 0.008128401917656826 0.09660889512339542 chr13 115169878 379790 0.0032976504498858634 0.061811009523175205 chr14 107349540 1024593 0.009544456361899642 0.10505720339807793 chr15 102531392 444429 0.004334565164198688 0.07054542352156871 chr16 90354753 627143 0.006940896623335355 0.0930205550345115 chr17 81195210 930277 0.011457289167673808 0.11842776867538139 chr18 78077248 606431 0.0077670642284932995 0.10310245489666701 chr19 59128983 627184 0.010607048661736665 0.12541462608357465 chr20 63025520 611813 0.009707385198884515 0.10839628332636157 chr21 48129895 325111 0.006754866180364616 0.09149847793864133 chr22 51304566 263547 0.0051369112059148885 0.07781498467096856 chrMT 16571 2679 0.16166797417174583 0.43529428139034115 chrX 155270560 709684 0.004570628198932238 0.07357712591263424 chrY 59373566 73218 0.001233175046282381 0.044382381115919634