BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080655.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,756,609 number of mapped reads = 1,591,790 (90.62%) number of supplementary alignments = 12,911 (0.73%) number of secondary alignments = 0 number of mapped bases = 105,044,915 bp number of sequenced bases = 105,006,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,771 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2338 >>>>>>> ACTG content number of A's = 28,033,995 bp (26.7%) number of C's = 19,642,606 bp (18.71%) number of T's = 32,943,784 bp (31.37%) number of G's = 24,381,555 bp (23.22%) number of N's = 4,536 bp (0%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 714,715 number of insertions = 7,857 mapped reads with insertion percentage = 0.49% number of deletions = 23,991 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.83% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.2686X There is a 2.89% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12707406 0.05098244469368845 0.307062942235007 chr2 243199373 6931791 0.02850250358170126 0.42814085910317884 chr3 198022430 6440313 0.032523149019027794 0.20470317452013148 chr4 191154276 4469248 0.023380319255845473 0.177884096213613 chr5 180915260 5088925 0.028128776975474595 0.19138311084512621 chr6 171115067 6274694 0.03666944185575429 0.2571669987749381 chr7 159138663 6669038 0.04190708828564181 0.49310604212876735 chr8 146364022 12394148 0.0846802911715558 0.36445151450022273 chr9 141213431 3296036 0.023340810974276236 0.20831207932468776 chr10 135534747 5128491 0.03783893882208671 0.23538320872561533 chr11 135006516 4351464 0.03223151095907104 0.21323283931033327 chr12 133851895 3449548 0.02577137962820773 0.18378552966629516 chr13 115169878 2033559 0.01765703876147199 0.15172593657315508 chr14 107349540 2032512 0.018933588350727913 0.1588989667438849 chr15 102531392 1952695 0.019044850185980115 0.1664186474925933 chr16 90354753 2644225 0.029264924225956324 0.1998941919081744 chr17 81195210 1800081 0.022169793021041512 0.17061773177435535 chr18 78077248 3349708 0.04290248549743966 0.27510932054286247 chr19 59128983 1650039 0.0279057564714076 0.22501950019942066 chr20 63025520 2775372 0.04403568586185406 0.24313318392959984 chr21 48129895 1470720 0.03055730746971295 0.20184041014711954 chr22 51304566 1116453 0.021761279493135173 0.16740157142772938 chrMT 16571 17589 1.061432623257498 1.2472123326423916 chrX 155270560 6793902 0.04375524890230318 0.24473635920321477 chrY 59373566 206958 0.0034856926060327924 0.07056639223512226