BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080650.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 = 1,413,611 number of mapped reads = 1,276,180 (90.28%) number of supplementary alignments = 11,730 (0.83%) number of secondary alignments = 0 number of mapped bases = 83,942,144 bp number of sequenced bases = 83,911,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,901 duplication rate = 2.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0996 >>>>>>> ACTG content number of A's = 22,420,033 bp (26.72%) number of C's = 15,491,024 bp (18.46%) number of T's = 26,557,335 bp (31.65%) number of G's = 19,439,162 bp (23.17%) number of N's = 3,555 bp (0%) GC percentage = 41.63% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 573,841 number of insertions = 6,193 mapped reads with insertion percentage = 0.48% number of deletions = 19,488 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.97% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2211X There is a 2.39% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10262000 0.04117141196611101 0.2533548501039177 chr2 243199373 5792632 0.02381844956483502 0.34085032672717236 chr3 198022430 5081591 0.025661693980828335 0.1763109828326398 chr4 191154276 3510062 0.01836245609279491 0.15257359227986902 chr5 180915260 3874957 0.02141862991546429 0.16128631707391014 chr6 171115067 5096773 0.029785647104939042 0.2297198719978967 chr7 159138663 5249472 0.032986779586051944 0.3629460787828552 chr8 146364022 9823823 0.06711911073337408 0.31032649696963094 chr9 141213431 2750784 0.01947962017862168 0.1653476119359441 chr10 135534747 3873338 0.028578191834452607 0.19692250154775176 chr11 135006516 3651298 0.02704534646312923 0.19124711189564644 chr12 133851895 2689466 0.020092849638027165 0.15741544846663877 chr13 115169878 1799746 0.015626881188499652 0.14014517914500083 chr14 107349540 1604062 0.014942420805901916 0.13569910300063986 chr15 102531392 1577870 0.015389140527810253 0.14631687597583132 chr16 90354753 2046978 0.022654901176034425 0.16941289366804177 chr17 81195210 1441848 0.017757796303501154 0.14930162666064745 chr18 78077248 2561709 0.03280992946882554 0.24022429818202426 chr19 59128983 1374596 0.023247414892963742 0.18015998375224146 chr20 63025520 2137045 0.033907613931626425 0.20562551222836264 chr21 48129895 1213589 0.025214869053838577 0.1774656036427024 chr22 51304566 846702 0.01650344337772977 0.1408659587183286 chrMT 16571 6336 0.3823547160702432 0.6882463014027326 chrX 155270560 5506346 0.03546291067669235 0.21493957952539586 chrY 59373566 169121 0.002848422478110882 0.061348117975417275