BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238638.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 = 2,929,050 number of mapped reads = 2,560,329 (87.41%) number of supplementary alignments = 20,384 (0.7%) number of secondary alignments = 0 number of mapped bases = 158,234,374 bp number of sequenced bases = 158,160,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,169,673 duplication rate = 22.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6225 >>>>>>> ACTG content number of A's = 39,311,138 bp (24.86%) number of C's = 27,169,042 bp (17.18%) number of T's = 54,038,012 bp (34.17%) number of G's = 37,638,415 bp (23.8%) number of N's = 3,746 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 847,357 number of insertions = 10,483 mapped reads with insertion percentage = 0.41% number of deletions = 43,638 mapped reads with deletion percentage = 1.69% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.0511X std coverageData = 0.9468X There is a 1.06% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.19% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 34984691 0.14035949382850285 1.3212917162830684 chr2 243199373 5388992 0.02215874133853133 1.4582014856565908 chr3 198022430 12563287 0.06344375735617425 0.905395721065372 chr4 191154276 23297167 0.12187625350321747 1.2074886506032703 chr5 180915260 3085692 0.017056007326302934 0.41781033184197963 chr6 171115067 17016573 0.0994452054885383 1.2029805071292712 chr7 159138663 3452825 0.021696958708268148 0.5867100148383063 chr8 146364022 3765297 0.025725563895750283 0.7152732422660172 chr9 141213431 6099843 0.04319591243413667 0.7145301009115057 chr10 135534747 13346102 0.09846996652452526 1.0860164945326718 chr11 135006516 2928884 0.021694389921150175 0.48267310377929656 chr12 133851895 4171164 0.03116253228988652 0.5950915718147085 chr13 115169878 6694672 0.05812867145695856 0.893537953670493 chr14 107349540 2519400 0.023469127115030023 0.5481608771237937 chr15 102531392 2348405 0.022904253557778677 0.5768583717102245 chr16 90354753 1862726 0.020615694671867454 0.4961084030018824 chr17 81195210 2037265 0.025090950562231443 0.5093846094316978 chr18 78077248 1794699 0.022986196952023717 2.054196724738937 chr19 59128983 2088529 0.0353215782520731 0.6567698518849178 chr20 63025520 1856623 0.02945827341051688 0.5935074621662167 chr21 48129895 1220554 0.025359581607231847 0.5315193571239893 chr22 51304566 2066856 0.040286004953243346 0.6565394282148177 chrMT 16571 43422 2.6203608714018465 5.283005141808152 chrX 155270560 3250889 0.020936930993228853 0.4675546713799716 chrY 59373566 349817 0.005891797033043291 0.36034348971344454