BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238665.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 = 8,797,305 number of mapped reads = 8,209,583 (93.32%) number of supplementary alignments = 68,506 (0.78%) number of secondary alignments = 0 number of mapped bases = 515,386,999 bp number of sequenced bases = 515,176,822 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 856,208 duplication rate = 8.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0158 >>>>>>> ACTG content number of A's = 127,761,161 bp (24.8%) number of C's = 93,843,052 bp (18.22%) number of T's = 165,588,504 bp (32.14%) number of G's = 127,957,576 bp (24.84%) number of N's = 26,529 bp (0.01%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 2,807,990 number of insertions = 39,276 mapped reads with insertion percentage = 0.47% number of deletions = 118,697 mapped reads with deletion percentage = 1.43% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.1665X std coverageData = 1.5703X There is a 11.85% of reference with a coverageData >= 1X There is a 2.92% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 43214966 0.17337957204126686 2.660157946784643 chr2 243199373 40469551 0.16640483279535428 2.866561849760842 chr3 198022430 33563947 0.16949568288804456 0.5851424970514112 chr4 191154276 32425527 0.16963014209527805 0.680017468169511 chr5 180915260 32495510 0.1796172970704627 0.6293057443067698 chr6 171115067 31208498 0.18238310948970962 1.1135571271151432 chr7 159138663 27009863 0.1697253356967062 2.04376166444591 chr8 146364022 23117205 0.1579432204999122 1.2830536391318041 chr9 141213431 22411315 0.1587052650820445 1.5061854549109048 chr10 135534747 22965006 0.16943998869898655 1.296400797584652 chr11 135006516 21544201 0.15957897172903862 1.273083703782706 chr12 133851895 24283833 0.18142315430050504 0.6804734753945606 chr13 115169878 14940629 0.12972688049561015 0.698567734482911 chr14 107349540 15584251 0.1451729648771667 0.7795732071174067 chr15 102531392 14705617 0.1434255081604666 0.7489352853877019 chr16 90354753 15849276 0.17541164657934485 0.8714607872254596 chr17 81195210 15169346 0.18682562678266365 0.7203409397649817 chr18 78077248 14600235 0.18699730554027724 3.657918338410248 chr19 59128983 12880132 0.21783110999896615 1.6788395798046507 chr20 63025520 10952160 0.17377341749818168 0.6728123957594546 chr21 48129895 6739221 0.14002151885018657 0.7035939090430057 chr22 51304566 6448925 0.12569885105353001 0.49107186585376744 chrMT 16571 37577 2.2676362319715166 2.7095957951155234 chrX 155270560 31328988 0.20177030339814578 0.8449300955312562 chrY 59373566 1441220 0.02427376519712493 0.544877746426281