BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238616.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 = 3,431,370 number of mapped reads = 1,947,163 (56.75%) number of supplementary alignments = 14,126 (0.41%) number of secondary alignments = 0 number of mapped bases = 118,126,367 bp number of sequenced bases = 118,076,463 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 572,139 duplication rate = 20.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0628 >>>>>>> ACTG content number of A's = 28,728,615 bp (24.33%) number of C's = 20,854,906 bp (17.66%) number of T's = 39,570,478 bp (33.51%) number of G's = 28,916,771 bp (24.49%) number of N's = 5,693 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 663,893 number of insertions = 7,665 mapped reads with insertion percentage = 0.39% number of deletions = 29,161 mapped reads with deletion percentage = 1.48% homopolymer indels = 42.44% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.5678X There is a 1.74% of reference with a coverageData >= 1X There is a 0.81% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% 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% 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 7807862 0.03132534622651953 0.4891683676275862 chr2 243199373 9073498 0.03730888730539614 1.217390207074101 chr3 198022430 7484736 0.03779741517160455 0.3811057361966281 chr4 191154276 11440965 0.059851996195994066 0.4872994534605808 chr5 180915260 7905323 0.043696275261688816 0.4130222173956048 chr6 171115067 5283320 0.03087583164140654 0.5551849851936553 chr7 159138663 5418923 0.034051580538916555 0.46135968378746506 chr8 146364022 6704183 0.04580485633279468 0.4902922848440173 chr9 141213431 4600109 0.03257557703558665 0.3669218727366723 chr10 135534747 9941294 0.07334867419644056 0.5825454826802344 chr11 135006516 5326149 0.039451051384808714 0.4188087769023452 chr12 133851895 4623670 0.034543179235527445 0.37986833605166226 chr13 115169878 2710740 0.023536883489622174 0.40702708910133106 chr14 107349540 5100790 0.04751571362112963 0.44981808707493764 chr15 102531392 2796031 0.027269999416373866 0.40351540364607963 chr16 90354753 3784726 0.041887403532606636 0.4534598516475886 chr17 81195210 2955559 0.036400657132360396 0.38484859385272174 chr18 78077248 2594162 0.03322558192624822 1.095130019556096 chr19 59128983 1857979 0.031422475167550236 0.43862841919624884 chr20 63025520 2188579 0.034725282710876486 0.3694452067352331 chr21 48129895 1397154 0.029028818783003785 0.3513562105110728 chr22 51304566 1138038 0.02218200228026488 0.2907407381547576 chrMT 16571 287023 17.320801400036206 12.05035858046543 chrX 155270560 5355094 0.03448879169367329 0.36065892949965145 chrY 59373566 350460 0.005902626768282707 0.23234178003757142