BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971305.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,668,941 number of mapped reads = 8,187,534 (84.68%) number of secondary alignments = 0 number of mapped bases = 322,915,415 bp number of sequenced bases = 322,882,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 465,816 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3852 >>>>>>> ACTG content number of A's = 94,193,175 bp (29.17%) number of C's = 65,589,196 bp (20.31%) number of T's = 96,051,943 bp (29.75%) number of G's = 67,032,443 bp (20.76%) number of N's = 15,288 bp (0%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 957,452 number of insertions = 11,493 mapped reads with insertion percentage = 0.14% number of deletions = 26,696 mapped reads with deletion percentage = 0.33% homopolymer indels = 40.37% >>>>>>> Coverage mean coverageData = 0.1043X std coverageData = 0.837X There is a 8.35% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 25565688 0.10257020783912109 1.370696536957952 chr2 243199373 27384296 0.11260019161315847 0.6986600748735267 chr3 198022430 23109794 0.1167029108773183 0.4107624414013705 chr4 191154276 22442822 0.11740685309074644 0.48027616388005007 chr5 180915260 20800504 0.11497373963921009 0.4145460027298631 chr6 171115067 19723187 0.11526271383220742 0.43319452907950673 chr7 159138663 18308920 0.11505010570561347 1.2036128618859232 chr8 146364022 17233532 0.11774431834074633 2.0448099887829487 chr9 141213431 13579171 0.09616061945269215 0.6694879652278561 chr10 135534747 15738748 0.11612334363231593 0.8186981745855161 chr11 135006516 15024543 0.11128753963253152 0.6438512586657189 chr12 133851895 15057764 0.11249571027739279 0.4197878674728683 chr13 115169878 10895516 0.09460386855667244 0.36034164108823596 chr14 107349540 10164903 0.09468976765061127 0.46206800800063086 chr15 102531392 9190496 0.08963592340577996 0.3525050434590714 chr16 90354753 8664169 0.09589057257452743 0.451762285298917 chr17 81195210 7858819 0.09678919483058175 0.42902921472360084 chr18 78077248 9998784 0.12806271040700615 1.2532285785943744 chr19 59128983 5612684 0.09492272173867763 1.2908308297842785 chr20 63025520 6383063 0.1012774349184267 0.4068848644682609 chr21 48129895 4184121 0.08693393160321668 0.4478385542818122 chr22 51304566 3205996 0.06248948680318239 0.29959195366552016 chrMT 16571 26784 1.6163176633878462 1.8356986167590859 chrX 155270560 11677674 0.07520855209126573 0.4185662536817548 chrY 59373566 1083437 0.01824780071319954 0.34204036211143873