BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716421.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 = 1,347,571 number of mapped reads = 1,237,848 (91.86%) number of supplementary alignments = 4,431 (0.33%) number of secondary alignments = 0 number of mapped bases = 71,718,753 bp number of sequenced bases = 71,696,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,287 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5132 >>>>>>> ACTG content number of A's = 18,631,903 bp (25.99%) number of C's = 14,502,293 bp (20.23%) number of T's = 22,070,830 bp (30.78%) number of G's = 16,490,043 bp (23%) number of N's = 1,340 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 358,526 number of insertions = 5,911 mapped reads with insertion percentage = 0.48% number of deletions = 13,784 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.24% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2337X There is a 2.11% of reference with a coverageData >= 1X There is a 0.14% 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 6035985 0.024216529434444217 0.35216694719572683 chr2 243199373 5659363 0.023270467066541328 0.34368702703256837 chr3 198022430 3736045 0.01886677685957091 0.1490607772976674 chr4 191154276 4455655 0.023309209154180784 0.19885767637502136 chr5 180915260 4073731 0.022517343202557927 0.16096134616088467 chr6 171115067 3798071 0.022196005685460766 0.18341253655724024 chr7 159138663 4091904 0.025712821277127356 0.2823546793290114 chr8 146364022 3806752 0.026008796068749736 0.3018759844813432 chr9 141213431 2407086 0.017045729878201174 0.16333590953290728 chr10 135534747 3172564 0.02340775388026511 0.2551201571120063 chr11 135006516 2559641 0.018959388597214077 0.18401455736529065 chr12 133851895 3603985 0.026925169793076145 0.17746701420033398 chr13 115169878 2170961 0.018850076406263103 0.14838889667364213 chr14 107349540 2410470 0.02245440455543638 0.1626931947229784 chr15 102531392 2628447 0.025635534139632085 0.1721496230938736 chr16 90354753 2505489 0.027729465432770314 0.18751618532224076 chr17 81195210 3205185 0.03947505031392862 0.22258015050041463 chr18 78077248 1343600 0.017208598335842984 0.26459530110622925 chr19 59128983 1874186 0.03169657086779253 0.2943149747624761 chr20 63025520 2386798 0.03787034204557138 0.21732885166810367 chr21 48129895 931576 0.01935545465037894 0.18174512359250378 chr22 51304566 685559 0.013362533853224681 0.12422147469999455 chrMT 16571 9163 0.552953955705751 0.8757313318048946 chrX 155270560 3884014 0.02501449083457933 0.1825850452697201 chrY 59373566 282523 0.0047583970280646445 0.21702725427514027