BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038409.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 = 83,224,894 number of mapped reads = 82,939,211 (99.66%) number of supplementary alignments = 204,461 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 41,528,586 number of mapped paired reads (second in pair) = 41,410,625 number of mapped paired reads (both in pair) = 82,795,752 number of mapped paired reads (singletons) = 143,459 number of mapped bases = 12,358,155,566 bp number of sequenced bases = 12,355,753,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,276,548 duplication rate = 35.97% >>>>>>> Insert size mean insert size = 26,500.2928 std insert size = 1,719,283.0301 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.826 >>>>>>> ACTG content number of A's = 3,069,678,246 bp (24.84%) number of C's = 3,113,613,856 bp (25.2%) number of T's = 3,092,407,969 bp (25.03%) number of G's = 3,078,859,631 bp (24.92%) number of N's = 1,193,542 bp (0.01%) GC percentage = 50.12% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 56,092,589 number of insertions = 708,702 mapped reads with insertion percentage = 0.81% number of deletions = 847,339 mapped reads with deletion percentage = 0.99% homopolymer indels = 46.61% >>>>>>> Coverage mean coverageData = 3.992X std coverageData = 25.3855X There is a 26.22% of reference with a coverageData >= 1X There is a 16.9% of reference with a coverageData >= 2X There is a 11.06% of reference with a coverageData >= 3X There is a 8.51% of reference with a coverageData >= 4X There is a 6.73% of reference with a coverageData >= 5X There is a 5.72% of reference with a coverageData >= 6X There is a 5.02% of reference with a coverageData >= 7X There is a 4.57% of reference with a coverageData >= 8X There is a 4.25% of reference with a coverageData >= 9X There is a 4.03% of reference with a coverageData >= 10X There is a 3.85% of reference with a coverageData >= 11X There is a 3.72% of reference with a coverageData >= 12X There is a 3.61% of reference with a coverageData >= 13X There is a 3.51% of reference with a coverageData >= 14X There is a 3.43% of reference with a coverageData >= 15X There is a 3.36% of reference with a coverageData >= 16X There is a 3.29% of reference with a coverageData >= 17X There is a 3.23% of reference with a coverageData >= 18X There is a 3.18% of reference with a coverageData >= 19X There is a 3.12% of reference with a coverageData >= 20X There is a 3.07% of reference with a coverageData >= 21X There is a 3.03% of reference with a coverageData >= 22X There is a 2.98% of reference with a coverageData >= 23X There is a 2.94% of reference with a coverageData >= 24X There is a 2.89% of reference with a coverageData >= 25X There is a 2.85% of reference with a coverageData >= 26X There is a 2.81% of reference with a coverageData >= 27X There is a 2.78% of reference with a coverageData >= 28X There is a 2.74% of reference with a coverageData >= 29X There is a 2.7% of reference with a coverageData >= 30X There is a 2.67% of reference with a coverageData >= 31X There is a 2.64% of reference with a coverageData >= 32X There is a 2.6% of reference with a coverageData >= 33X There is a 2.57% of reference with a coverageData >= 34X There is a 2.54% of reference with a coverageData >= 35X There is a 2.51% of reference with a coverageData >= 36X There is a 2.48% of reference with a coverageData >= 37X There is a 2.45% of reference with a coverageData >= 38X There is a 2.42% of reference with a coverageData >= 39X There is a 2.39% of reference with a coverageData >= 40X There is a 2.36% of reference with a coverageData >= 41X There is a 2.34% of reference with a coverageData >= 42X There is a 2.31% of reference with a coverageData >= 43X There is a 2.28% of reference with a coverageData >= 44X There is a 2.26% of reference with a coverageData >= 45X There is a 2.23% of reference with a coverageData >= 46X There is a 2.21% of reference with a coverageData >= 47X There is a 2.18% of reference with a coverageData >= 48X There is a 2.16% of reference with a coverageData >= 49X There is a 2.13% of reference with a coverageData >= 50X There is a 2.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1112193055 4.4621475787617 25.611346550645766 chr2 243199373 1022402002 4.203966438679922 28.35265550913501 chr3 198022430 629806891 3.18048258977531 19.96138673179753 chr4 191154276 414498321 2.168396803218778 15.721441124644896 chr5 180915260 530898271 2.9345134899068217 20.993579361369232 chr6 171115067 774185379 4.524355409334001 29.300055830052234 chr7 159138663 659461724 4.143944102383215 28.304123503015056 chr8 146364022 402910331 2.7527962507070214 18.578706889388272 chr9 141213431 464913587 3.29227598046251 21.522038247247156 chr10 135534747 418277347 3.08612629793008 18.64788659229255 chr11 135006516 758565764 5.618734461675909 32.06643093813517 chr12 133851895 559190173 4.177678418374279 22.772355903076324 chr13 115169878 398995680 3.4644100256839727 27.636024067150725 chr14 107349540 305107774 2.842189859406943 17.67349297843004 chr15 102531392 337069192 3.287473089217398 18.82016992786269 chr16 90354753 627623828 6.9462181806860785 35.24132753849699 chr17 81195210 811041545 9.988785606934202 41.93357132116457 chr18 78077248 125194707 1.6034723329387839 11.534569625676902 chr19 59128983 839027636 14.189786352320654 49.63879377076698 chr20 63025520 447220333 7.095861057552559 39.188606603732744 chr21 48129895 105191117 2.1855671407552415 24.98251544419695 chr22 51304566 211050879 4.113686080104449 21.11321307473606 chrMT 16571 1754367 105.86971214772795 36.459745713933465 chrX 155270560 374996227 2.4151147970355744 17.79650748332555 chrY 59373566 26579436 0.4476644707511757 6.000395840693706