BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549032.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 5,393,220 number of mapped reads = 4,571,027 (84.76%) number of secondary alignments = 0 number of mapped bases = 180,772,109 bp number of sequenced bases = 180,752,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,995 duplication rate = 5.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.0803 >>>>>>> ACTG content number of A's = 51,557,388 bp (28.52%) number of C's = 38,453,235 bp (21.27%) number of T's = 52,070,553 bp (28.81%) number of G's = 38,669,558 bp (21.39%) number of N's = 1,919 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 496,501 number of insertions = 5,892 mapped reads with insertion percentage = 0.13% number of deletions = 14,757 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.86% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.9456X There is a 3.45% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 14154967 0.056790097225073714 0.7580598407381112 chr2 243199373 16830819 0.06920584865159171 0.49034361067893184 chr3 198022430 12462419 0.06293438071636633 0.3871702430315037 chr4 191154276 11222052 0.058706779857752175 0.38582155163918297 chr5 180915260 11625176 0.06425757561855203 0.39466340590122034 chr6 171115067 9498326 0.05550841411294308 0.366683914070458 chr7 159138663 9408585 0.059121930664957266 0.5232736428704851 chr8 146364022 9147279 0.0624967726016712 3.7991887055563422 chr9 141213431 7386338 0.05230620025088124 0.4203681477370353 chr10 135534747 8914196 0.06577055845317659 0.465699705282446 chr11 135006516 8419045 0.062360286373140686 0.5346874490024909 chr12 133851895 8307029 0.06206134773063915 0.3880870541575732 chr13 115169878 5027819 0.043655677051251195 0.3213293650783486 chr14 107349540 5578895 0.05196943554671962 0.38104953547959075 chr15 102531392 5434723 0.05300545417348864 0.3509639769660708 chr16 90354753 5315517 0.0588294121063006 0.39011643469350393 chr17 81195210 5195202 0.06398409462824223 0.4195494568735256 chr18 78077248 4287581 0.05491460201056267 0.702459286952342 chr19 59128983 4284199 0.0724551443747984 0.6927061158675922 chr20 63025520 4134928 0.06560720165418707 0.40609983782649084 chr21 48129895 2499361 0.051929492054782166 0.3752828561951359 chr22 51304566 2237393 0.04361001708892733 0.35486723752418226 chrMT 16571 86579 5.224729949912498 6.484973574887258 chrX 155270560 8687436 0.05595031021978667 0.3998602368224775 chrY 59373566 626245 0.010547538950245973 0.212681858731997