BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819023.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 = 1,870,836 number of mapped reads = 1,750,291 (93.56%) number of supplementary alignments = 25,446 (1.36%) number of secondary alignments = 0 number of mapped bases = 162,149,223 bp number of sequenced bases = 162,053,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 723,259 duplication rate = 33.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2754 >>>>>>> ACTG content number of A's = 45,767,019 bp (28.24%) number of C's = 34,058,901 bp (21.02%) number of T's = 46,422,522 bp (28.65%) number of G's = 35,797,369 bp (22.09%) number of N's = 7,938 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 986,818 number of insertions = 24,536 mapped reads with insertion percentage = 1.37% number of deletions = 51,798 mapped reads with deletion percentage = 2.9% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0524X std coverageData = 0.6089X There is a 2.63% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% 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% 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 16312816 0.0654474437598292 1.0184143953812743 chr2 243199373 13274103 0.0545811563420437 0.8356755152608626 chr3 198022430 8760831 0.04424160939748088 0.3715790537756504 chr4 191154276 9047136 0.04732897526184557 0.43262805710496655 chr5 180915260 8767648 0.04846273332608869 0.39964441137880546 chr6 171115067 6754062 0.03947087838851736 0.4225250672422802 chr7 159138663 8125845 0.051061413026952475 0.7724914709139737 chr8 146364022 14979139 0.10234167383019852 0.629934552368389 chr9 141213431 7054234 0.04995441262240842 0.5859074560356623 chr10 135534747 8424862 0.06216016325319145 0.7104746972162963 chr11 135006516 5540223 0.04103670818377388 0.424685565031401 chr12 133851895 7378619 0.055125248693714796 0.4243916976557499 chr13 115169878 3580157 0.031085879938155356 0.30972637048643975 chr14 107349540 3846892 0.03583519780336274 0.3566341424454872 chr15 102531392 4213531 0.041095033606878176 0.35890087838468854 chr16 90354753 5002265 0.055362499856537704 0.6492596362370161 chr17 81195210 5531056 0.06812047163865947 0.5239385799359728 chr18 78077248 3840036 0.049182522416773705 0.6769065143486844 chr19 59128983 3405155 0.05758859407407701 0.9720919401273148 chr20 63025520 4386391 0.06959706163471559 0.4955342847285292 chr21 48129895 2257673 0.046907914509267054 0.4101900447257155 chr22 51304566 1210436 0.02359314373695316 0.30665329629017163 chrMT 16571 45268 2.731760304145797 3.105928543293336 chrX 155270560 9841728 0.063384378854562 0.5221110625495258 chrY 59373566 569117 0.009585359922629542 0.5303812358807456