BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082969.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 = 3,531,706 number of mapped reads = 3,042,839 (86.16%) number of supplementary alignments = 15,210 (0.43%) number of secondary alignments = 0 number of mapped bases = 201,187,192 bp number of sequenced bases = 201,112,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,697 duplication rate = 5.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6786 >>>>>>> ACTG content number of A's = 55,012,531 bp (27.35%) number of C's = 36,293,091 bp (18.05%) number of T's = 65,292,188 bp (32.47%) number of G's = 44,494,737 bp (22.12%) number of N's = 19,720 bp (0.01%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,725,950 number of insertions = 15,914 mapped reads with insertion percentage = 0.52% number of deletions = 43,970 mapped reads with deletion percentage = 1.43% homopolymer indels = 48.38% >>>>>>> Coverage mean coverageData = 0.065X std coverageData = 0.4607X There is a 4.91% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15937881 0.0639431947493523 0.6795995922753677 chr2 243199373 17192785 0.07069419952822 0.6158491196795717 chr3 198022430 13210016 0.06670969546227667 0.3284924961556561 chr4 191154276 13627464 0.07129039582666725 0.3512884861067211 chr5 180915260 13196463 0.07294278547868212 0.3485913740008929 chr6 171115067 11933573 0.06974004808121309 0.37549383268608416 chr7 159138663 11083274 0.06964538843712668 0.6601581883260134 chr8 146364022 10327464 0.07056012713288243 0.5128486731967549 chr9 141213431 8119060 0.057494955986162534 0.47013195066427993 chr10 135534747 9098714 0.06713196579767106 0.3713567839965961 chr11 135006516 8981931 0.06652961105966174 0.4039989479111999 chr12 133851895 9102946 0.06800759899589019 0.3376479826480144 chr13 115169878 7115541 0.06178300371213383 0.3199759669182592 chr14 107349540 6250766 0.058228158220333316 0.3262149333089866 chr15 102531392 5652598 0.05513041313239949 0.3002081453187346 chr16 90354753 5255007 0.05815971850423851 0.3469841478871493 chr17 81195210 4945823 0.06091274349804625 0.3363760029675543 chr18 78077248 5553210 0.07112456115256521 0.8161780993562684 chr19 59128983 3403434 0.05755948821240507 0.5508034071757127 chr20 63025520 4105268 0.06513659863496564 0.33849940191221867 chr21 48129895 2572513 0.053449379019006794 0.3119052409773725 chr22 51304566 2081580 0.04057299695313669 0.2536201567831154 chrMT 16571 76783 4.633576730432684 4.92905036768337 chrX 155270560 11914051 0.07673090764920279 0.3875600156484845 chrY 59373566 449047 0.007563079502416951 0.15711515135438525