BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084876.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 = 2,630,326 number of mapped reads = 2,337,779 (88.88%) number of supplementary alignments = 16,685 (0.63%) number of secondary alignments = 0 number of mapped bases = 161,801,361 bp number of sequenced bases = 161,740,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 104,574 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.7208 >>>>>>> ACTG content number of A's = 47,104,368 bp (29.12%) number of C's = 29,544,730 bp (18.27%) number of T's = 51,917,077 bp (32.1%) number of G's = 33,148,704 bp (20.49%) number of N's = 25,780 bp (0.02%) GC percentage = 38.76% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,292,618 number of insertions = 12,678 mapped reads with insertion percentage = 0.54% number of deletions = 34,371 mapped reads with deletion percentage = 1.45% homopolymer indels = 49.13% >>>>>>> Coverage mean coverageData = 0.0523X std coverageData = 0.3626X There is a 4.36% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.11% 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 12895804 0.05173830238922454 0.5901190575532509 chr2 243199373 12995987 0.05343758431482469 0.4051342361519781 chr3 198022430 13821408 0.06979718408667139 0.3057303084564262 chr4 191154276 10410323 0.05446031978902737 0.2706567973135636 chr5 180915260 8938439 0.04940677198816728 0.2622271588608309 chr6 171115067 10113316 0.05910242842613035 0.285288224284856 chr7 159138663 9649033 0.06063286456038656 0.3928999970587854 chr8 146364022 8286427 0.05661519058283326 0.5861074519972672 chr9 141213431 9769192 0.06918033172071289 0.39793328496137476 chr10 135534747 4961759 0.036608759818616846 0.2688278773436453 chr11 135006516 7257015 0.053753072185049204 0.32753515033731284 chr12 133851895 6751555 0.05044048872076111 0.2604713667011467 chr13 115169878 4895267 0.042504751112092 0.23599127720928875 chr14 107349540 3251893 0.030292565762275275 0.20991432589041634 chr15 102531392 4033807 0.03934216556818033 0.22840390597978955 chr16 90354753 2776485 0.03072870997721614 0.22046772877092943 chr17 81195210 3720500 0.04582166854424048 0.2540536271605561 chr18 78077248 6860862 0.08787274367047364 0.6087187908936137 chr19 59128983 3067416 0.05187669133426496 0.39685417583144006 chr20 63025520 2962113 0.0469986284920775 0.2559473289517497 chr21 48129895 1502222 0.031211827908621034 0.2129326078985221 chr22 51304566 923890 0.018007948844163305 0.15129413254765375 chrMT 16571 58880 3.5531953412588257 2.624793735601722 chrX 155270560 11560897 0.07445646489585662 0.33234545186334663 chrY 59373566 336871 0.005673753872219836 0.11934133137458003