BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008765.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 = 2,759,872 number of mapped reads = 2,346,496 (85.02%) number of supplementary alignments = 18,396 (0.67%) number of secondary alignments = 0 number of mapped bases = 148,204,657 bp number of sequenced bases = 148,146,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 242,570 duplication rate = 8.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.3664 >>>>>>> ACTG content number of A's = 38,973,007 bp (26.31%) number of C's = 25,542,944 bp (17.24%) number of T's = 48,928,792 bp (33.03%) number of G's = 34,647,262 bp (23.39%) number of N's = 54,299 bp (0.04%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,212,792 number of insertions = 9,214 mapped reads with insertion percentage = 0.39% number of deletions = 36,703 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.42% >>>>>>> Coverage mean coverageData = 0.0479X std coverageData = 0.3757X There is a 3.36% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 19096142 0.07661422035133064 0.3948324236214342 chr2 243199373 26342735 0.10831744619670546 0.5033454256361914 chr3 198022430 11917822 0.060184202365358305 0.34135290662606566 chr4 191154276 1451703 0.007594405055317726 0.11517442433570209 chr5 180915260 1201298 0.006640114272284162 0.10796602407442808 chr6 171115067 19991577 0.11683119055787179 0.570434152759218 chr7 159138663 12683477 0.07970078899054217 0.5175406795986335 chr8 146364022 16414120 0.11214586601070582 0.47768633657516457 chr9 141213431 3398373 0.024065508329728213 0.20835892356429195 chr10 135534747 6946592 0.05125321848278508 0.6352521664374758 chr11 135006516 11802259 0.08741992127254065 0.6619323181682158 chr12 133851895 8602464 0.06426852604514863 0.3381775890623943 chr13 115169878 581431 0.00504846414789117 0.10667348867854186 chr14 107349540 1432877 0.013347770283878254 0.15287754469545436 chr15 102531392 589344 0.0057479371781083395 0.09756791383841648 chr16 90354753 589308 0.006522158275392552 0.1403711865568681 chr17 81195210 716746 0.008827441914369086 0.25122952756059685 chr18 78077248 450884 0.005774844933059116 0.12701585283152064 chr19 59128983 478664 0.008095251697462816 0.11577581063555879 chr20 63025520 547694 0.008690035401532585 0.12423407494622181 chr21 48129895 251516 0.005225774957539384 0.10387595177562098 chr22 51304566 201706 0.003931540908074342 0.07661971720122804 chrMT 16571 408573 24.65590489409209 16.734595384795863 chrX 155270560 1952919 0.012577522744813956 0.197161059952595 chrY 59373566 154433 0.0026010396613199887 0.0652137464122012