BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038490.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,187,652 number of mapped reads = 13,889,433 (97.9%) number of supplementary alignments = 250,700 (1.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,019,502 number of mapped paired reads (second in pair) = 6,869,931 number of mapped paired reads (both in pair) = 13,725,154 number of mapped paired reads (singletons) = 164,279 number of mapped bases = 1,990,405,628 bp number of sequenced bases = 1,989,043,565 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,709,979 duplication rate = 8.22% >>>>>>> Insert size mean insert size = 86,784.0012 std insert size = 2,793,740.5154 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.8976 >>>>>>> ACTG content number of A's = 577,639,000 bp (29.04%) number of C's = 407,713,849 bp (20.5%) number of T's = 579,428,383 bp (29.13%) number of G's = 424,219,102 bp (21.33%) number of N's = 43,231 bp (0%) GC percentage = 41.83% >>>>>>> Mismatches and indels general error rate = 0.0133 number of mismatches = 25,520,438 number of insertions = 331,462 mapped reads with insertion percentage = 2.25% number of deletions = 658,570 mapped reads with deletion percentage = 4.56% homopolymer indels = 47.65% >>>>>>> Coverage mean coverageData = 0.643X std coverageData = 7.0435X There is a 28.51% of reference with a coverageData >= 1X There is a 14.68% of reference with a coverageData >= 2X There is a 7.46% of reference with a coverageData >= 3X There is a 4.19% of reference with a coverageData >= 4X There is a 2.35% of reference with a coverageData >= 5X There is a 1.38% of reference with a coverageData >= 6X There is a 0.83% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 133601811 0.5360139544045509 7.634300315864406 chr2 243199373 171774254 0.7063104311539488 7.181248381061948 chr3 198022430 132314852 0.668181134834069 1.392462770245385 chr4 191154276 113090376 0.5916183428719115 6.862404550993498 chr5 180915260 129527531 0.7159569126451798 1.559569638991786 chr6 171115067 145603592 0.85091041106275 8.667891196478646 chr7 159138663 141873218 0.8915069118055868 7.451416406575825 chr8 146364022 83819113 0.5726756606893462 1.8289781842336885 chr9 141213431 80938891 0.5731670877680183 9.68725713812529 chr10 135534747 85807986 0.6331069183314298 18.57516385402988 chr11 135006516 88816566 0.6578687357579096 3.180068458963285 chr12 133851895 72160515 0.5391071601937351 1.2440207715264295 chr13 115169878 123128267 1.0691013061592372 1.979255207467013 chr14 107349540 38385557 0.3575754213758159 1.0360587513702353 chr15 102531392 49904629 0.4867253630966017 1.1561324198199123 chr16 90354753 76357431 0.8450848291290222 12.983040053126315 chr17 81195210 50680425 0.6241799854942182 3.5813118622364017 chr18 78077248 28607860 0.3664045638493816 8.111419411675968 chr19 59128983 24709296 0.41788806007368673 4.244588743462492 chr20 63025520 70743662 1.1224605842204871 2.8264965865256935 chr21 48129895 16783096 0.348704188945353 3.07575641373804 chr22 51304566 13792381 0.2688334016898223 0.9212668728341004 chrMT 16571 1314019 79.29630076639913 34.49963216218979 chrX 155270560 93346536 0.6011863163242278 1.5718057751717798 chrY 59373566 23323764 0.39283077590454984 11.700006844327374