BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230374.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 = 2,118,901 number of mapped reads = 1,880,987 (88.77%) number of supplementary alignments = 15,626 (0.74%) number of secondary alignments = 0 number of mapped bases = 131,769,760 bp number of sequenced bases = 131,682,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,050 duplication rate = 2.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0928 >>>>>>> ACTG content number of A's = 39,851,941 bp (30.26%) number of C's = 25,946,518 bp (19.7%) number of T's = 38,084,591 bp (28.92%) number of G's = 27,726,953 bp (21.06%) number of N's = 72,033 bp (0.05%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 1,429,762 number of insertions = 12,645 mapped reads with insertion percentage = 0.67% number of deletions = 52,357 mapped reads with deletion percentage = 2.74% homopolymer indels = 45.61% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.4434X There is a 3.32% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7903275 0.03170814567398811 0.8138313307666409 chr2 243199373 13282744 0.054616686861277394 0.4752155809462387 chr3 198022430 8150135 0.04115763552644011 0.2494882773532542 chr4 191154276 9152346 0.04787936839037804 0.2995266168907458 chr5 180915260 8449665 0.04670509828745237 0.26937695998335914 chr6 171115067 7079354 0.04137189158217143 0.29081627245331637 chr7 159138663 7023050 0.04413163883373835 0.6072614466474796 chr8 146364022 6426109 0.043904976866514366 0.4387310433345572 chr9 141213431 4653214 0.03295163899813468 0.39431354922573053 chr10 135534747 4854139 0.035814719896145895 0.3970820328130906 chr11 135006516 7919720 0.0586617611849194 0.5581835963451921 chr12 133851895 6399062 0.04780703328854627 0.2739496087768373 chr13 115169878 3738728 0.03246272432449742 0.21994270717646816 chr14 107349540 5400270 0.05030547871933126 0.2938317438177974 chr15 102531392 5669580 0.05529604045559042 0.29097845277752804 chr16 90354753 2723039 0.030137197099083433 0.2864611777894159 chr17 81195210 3403242 0.04191431982256096 0.3154524209102954 chr18 78077248 3307331 0.042359728150254475 0.9337429668773308 chr19 59128983 2394905 0.04050306429251455 0.4945603504859033 chr20 63025520 2730077 0.04331700872916241 0.26766568016615194 chr21 48129895 1908720 0.03965768053306578 0.27901050125364724 chr22 51304566 1410122 0.027485311931105705 0.2006061587009524 chrMT 16571 4297 0.25930843039044116 0.562022514951453 chrX 155270560 7375788 0.0475028105778713 0.3082661206751822 chrY 59373566 410848 0.006919712385137857 0.19299651213478775