BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038406.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 = 18,142,256 number of mapped reads = 17,275,611 (95.22%) number of supplementary alignments = 253,010 (1.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,755,140 number of mapped paired reads (second in pair) = 8,520,471 number of mapped paired reads (both in pair) = 16,999,430 number of mapped paired reads (singletons) = 276,181 number of mapped bases = 2,343,820,638 bp number of sequenced bases = 2,342,232,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,268,340 duplication rate = 13.22% >>>>>>> Insert size mean insert size = 89,128.7198 std insert size = 2,909,877.1675 median insert size = 263 >>>>>>> Mapping quality mean mapping quality = 53.3959 >>>>>>> ACTG content number of A's = 670,279,701 bp (28.62%) number of C's = 464,083,650 bp (19.81%) number of T's = 681,734,226 bp (29.11%) number of G's = 525,950,599 bp (22.46%) number of N's = 184,270 bp (0.01%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 29,456,887 number of insertions = 404,349 mapped reads with insertion percentage = 2.23% number of deletions = 844,578 mapped reads with deletion percentage = 4.72% homopolymer indels = 48.56% >>>>>>> Coverage mean coverageData = 0.7571X std coverageData = 9.1896X There is a 28.06% of reference with a coverageData >= 1X There is a 16.39% of reference with a coverageData >= 2X There is a 9.63% of reference with a coverageData >= 3X There is a 6.04% of reference with a coverageData >= 4X There is a 3.82% of reference with a coverageData >= 5X There is a 2.48% of reference with a coverageData >= 6X There is a 1.64% of reference with a coverageData >= 7X There is a 1.1% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.53% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% 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 0.02% 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 215636188 0.8651380170483106 13.501038089482552 chr2 243199373 210315846 0.8647877805178388 10.410364283591488 chr3 198022430 163826970 0.8273152187860738 1.8372991499555673 chr4 191154276 91854782 0.48052695405045504 9.119264095565867 chr5 180915260 163980537 0.9063941703977874 1.8556521220647246 chr6 171115067 136865993 0.7998477013131754 7.516155150515244 chr7 159138663 113429369 0.7127706546083022 9.185792425564742 chr8 146364022 151088011 1.0322756162030038 3.7036287413478957 chr9 141213431 100828395 0.7140142002498332 15.981228813393415 chr10 135534747 122543680 0.904149546241452 21.07398704769209 chr11 135006516 108283414 0.8020606501689148 7.20872119408655 chr12 133851895 98717951 0.7375162749843773 1.830443065749908 chr13 115169878 80523160 0.6991685794787418 1.5842623840326366 chr14 107349540 78280612 0.7292123655117665 1.709351965241866 chr15 102531392 65090911 0.6348388501347958 1.5428839418177327 chr16 90354753 77504489 0.857779877943997 12.024346132010805 chr17 81195210 57279605 0.7054554696022093 11.428307822384602 chr18 78077248 94751804 1.2135648531054783 10.981659002634606 chr19 59128983 30277167 0.5120528962928383 5.708725527624978 chr20 63025520 63199432 1.002759390164492 3.558115850702481 chr21 48129895 22618557 0.4699481891660059 4.3255237738010255 chr22 51304566 13180900 0.2569147549167456 0.938073011340372 chrMT 16571 1573961 94.9828616257317 56.301320434929444 chrX 155270560 77862718 0.5014647850822461 2.0854233070367294 chrY 59373566 4306186 0.07252698953605044 9.20307043622037