BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238295.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 = 2,728,981 number of mapped reads = 2,487,918 (91.17%) number of supplementary alignments = 17,209 (0.63%) number of secondary alignments = 0 number of mapped bases = 161,085,583 bp number of sequenced bases = 161,002,249 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,309 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2797 >>>>>>> ACTG content number of A's = 42,556,647 bp (26.43%) number of C's = 30,003,638 bp (18.64%) number of T's = 49,971,420 bp (31.04%) number of G's = 38,434,306 bp (23.87%) number of N's = 36,238 bp (0.02%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,355,953 number of insertions = 12,426 mapped reads with insertion percentage = 0.5% number of deletions = 49,980 mapped reads with deletion percentage = 1.99% homopolymer indels = 44.82% >>>>>>> Coverage mean coverageData = 0.052X std coverageData = 0.4226X There is a 4.44% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% 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 11227703 0.045045837618996346 0.6096094206172616 chr2 243199373 14112635 0.05802907641542316 0.603238266345441 chr3 198022430 10769774 0.05438663690774828 0.2632442482323094 chr4 191154276 10634143 0.05563120649207973 0.29985214185089853 chr5 180915260 11440355 0.06323598683715238 0.2875764468299381 chr6 171115067 10043665 0.058695386537761754 0.35163759052673405 chr7 159138663 10459608 0.06572637851054461 0.6930733041883553 chr8 146364022 7895413 0.053943673398097795 0.4961197115401147 chr9 141213431 5089756 0.036043002170239744 0.38858192713326545 chr10 135534747 6681972 0.04930080402186459 0.38813301172372605 chr11 135006516 5570529 0.041261186237855366 0.3301234392471703 chr12 133851895 7215769 0.05390860547771849 0.26929081838701796 chr13 115169878 5837467 0.05068570967835878 0.25503519058243995 chr14 107349540 5423189 0.05051897753823631 0.2918576673317087 chr15 102531392 4970448 0.04847732877751235 0.2696425734484098 chr16 90354753 4906499 0.05430261095395834 0.3000656995731134 chr17 81195210 4330168 0.053330338082751436 0.2966782415533553 chr18 78077248 4496123 0.05758557217590456 0.7531155157758236 chr19 59128983 3042929 0.051462562784142594 0.4557286166840589 chr20 63025520 2918068 0.04629978459519255 0.2631110239898363 chr21 48129895 1982026 0.041180767171837794 0.265580356320635 chr22 51304566 2013367 0.039243427183459655 0.2252696231386986 chrMT 16571 6815 0.4112606360509323 0.7741157865977527 chrX 155270560 9572654 0.06165144248851811 0.3324380451847319 chrY 59373566 444508 0.007486631340283654 0.1919734420639254