BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819102.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,058,383 number of mapped reads = 958,657 (90.58%) number of supplementary alignments = 3,972 (0.38%) number of secondary alignments = 0 number of mapped bases = 55,261,142 bp number of sequenced bases = 55,243,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,333 duplication rate = 1.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0037 >>>>>>> ACTG content number of A's = 13,093,028 bp (23.7%) number of C's = 10,758,153 bp (19.47%) number of T's = 18,137,573 bp (32.83%) number of G's = 13,254,282 bp (23.99%) number of N's = 789 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 282,844 number of insertions = 3,815 mapped reads with insertion percentage = 0.4% number of deletions = 10,469 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.0179X std coverageData = 0.1841X There is a 1.66% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5411712 0.021711929857137647 0.3151889984667473 chr2 243199373 4359595 0.017926012498395708 0.201513212516796 chr3 198022430 3009636 0.015198460093636868 0.13018850197887993 chr4 191154276 3109117 0.01626496181545005 0.14330446888996615 chr5 180915260 3001932 0.01659302813925149 0.1365319120200232 chr6 171115067 2372599 0.013865517757124217 0.1463109641348275 chr7 159138663 2749466 0.017277171670092517 0.22212992288849256 chr8 146364022 5021078 0.0343054114760525 0.21488350298482392 chr9 141213431 2350677 0.01664627070777708 0.1630910849062944 chr10 135534747 2898796 0.021387843812480056 0.19438092909099086 chr11 135006516 1899300 0.01406820986329282 0.17084750682356403 chr12 133851895 2615387 0.019539409584003273 0.14760481800197695 chr13 115169878 1233417 0.010709545077402965 0.10941598747505347 chr14 107349540 1314869 0.01224848285330333 0.11885427990451776 chr15 102531392 1450663 0.0141484765953436 0.12813763441570222 chr16 90354753 1753343 0.019405099806979718 0.15408630150230407 chr17 81195210 1934960 0.02383096244224259 0.16706391716665253 chr18 78077248 1307619 0.01674775985956882 0.26435443048073776 chr19 59128983 1145694 0.019376183080977393 0.21726948568410445 chr20 63025520 1560693 0.024762873832695074 0.16692283676967212 chr21 48129895 755256 0.01569203506469316 0.1386152653172866 chr22 51304566 448757 0.008746921277922905 0.09864335950298228 chrMT 16571 51021 3.07893307585541 2.3952947971961405 chrX 155270560 3330593 0.02145025431736705 0.1687075144667486 chrY 59373566 174962 0.0029467995909155937 0.08342259431815957