BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504706.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 488,572,822 number of mapped reads = 442,647,689 (90.6%) number of supplementary alignments = 2,255,302 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 222,450,629 number of mapped paired reads (second in pair) = 220,197,060 number of mapped paired reads (both in pair) = 436,945,212 number of mapped paired reads (singletons) = 5,702,477 number of mapped bases = 43,485,290,393 bp number of sequenced bases = 43,476,091,476 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,163,932 duplication rate = 23.09% >>>>>>> Insert size mean insert size = 43,207.7617 std insert size = 1,936,494.3675 median insert size = 410 >>>>>>> Mapping quality mean mapping quality = 53.7988 >>>>>>> ACTG content number of A's = 11,519,344,087 bp (26.5%) number of C's = 10,118,989,125 bp (23.27%) number of T's = 11,537,828,693 bp (26.54%) number of G's = 10,287,129,128 bp (23.66%) number of N's = 12,800,443 bp (0.03%) GC percentage = 46.94% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 302,583,304 number of insertions = 3,404,908 mapped reads with insertion percentage = 0.75% number of deletions = 3,756,504 mapped reads with deletion percentage = 0.83% homopolymer indels = 40.5% >>>>>>> Coverage mean coverageData = 14.047X std coverageData = 33.4483X There is a 75.99% of reference with a coverageData >= 1X There is a 68.24% of reference with a coverageData >= 2X There is a 61.86% of reference with a coverageData >= 3X There is a 56.71% of reference with a coverageData >= 4X There is a 52.23% of reference with a coverageData >= 5X There is a 48.31% of reference with a coverageData >= 6X There is a 44.82% of reference with a coverageData >= 7X There is a 41.69% of reference with a coverageData >= 8X There is a 38.88% of reference with a coverageData >= 9X There is a 36.34% of reference with a coverageData >= 10X There is a 34.03% of reference with a coverageData >= 11X There is a 31.92% of reference with a coverageData >= 12X There is a 30% of reference with a coverageData >= 13X There is a 28.24% of reference with a coverageData >= 14X There is a 26.63% of reference with a coverageData >= 15X There is a 25.15% of reference with a coverageData >= 16X There is a 23.78% of reference with a coverageData >= 17X There is a 22.52% of reference with a coverageData >= 18X There is a 21.35% of reference with a coverageData >= 19X There is a 20.27% of reference with a coverageData >= 20X There is a 19.26% of reference with a coverageData >= 21X There is a 18.33% of reference with a coverageData >= 22X There is a 17.46% of reference with a coverageData >= 23X There is a 16.65% of reference with a coverageData >= 24X There is a 15.89% of reference with a coverageData >= 25X There is a 15.17% of reference with a coverageData >= 26X There is a 14.51% of reference with a coverageData >= 27X There is a 13.88% of reference with a coverageData >= 28X There is a 13.3% of reference with a coverageData >= 29X There is a 12.74% of reference with a coverageData >= 30X There is a 12.22% of reference with a coverageData >= 31X There is a 11.73% of reference with a coverageData >= 32X There is a 11.27% of reference with a coverageData >= 33X There is a 10.83% of reference with a coverageData >= 34X There is a 10.42% of reference with a coverageData >= 35X There is a 10.03% of reference with a coverageData >= 36X There is a 9.66% of reference with a coverageData >= 37X There is a 9.3% of reference with a coverageData >= 38X There is a 8.97% of reference with a coverageData >= 39X There is a 8.65% of reference with a coverageData >= 40X There is a 8.35% of reference with a coverageData >= 41X There is a 8.06% of reference with a coverageData >= 42X There is a 7.79% of reference with a coverageData >= 43X There is a 7.52% of reference with a coverageData >= 44X There is a 7.27% of reference with a coverageData >= 45X There is a 7.03% of reference with a coverageData >= 46X There is a 6.81% of reference with a coverageData >= 47X There is a 6.59% of reference with a coverageData >= 48X There is a 6.38% of reference with a coverageData >= 49X There is a 6.18% of reference with a coverageData >= 50X There is a 5.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3581999284 14.37107466223725 30.576773679072616 chr2 243199373 2972223482 12.221345167694984 23.093062290639228 chr3 198022430 2534161748 12.797346987409457 24.31288451395898 chr4 191154276 1867316913 9.768637940382773 17.473066678814362 chr5 180915260 2842141739 15.709795508681799 30.326425274761693 chr6 171115067 1314065645 7.67942687945767 15.318183182152781 chr7 159138663 2227463300 13.996996443284182 24.11312667263734 chr8 146364022 2445096845 16.705586602423374 32.93222072913796 chr9 141213431 1042335066 7.381274278365208 27.360237203452687 chr10 135534747 2955750556 21.808064879480686 34.90471288067238 chr11 135006516 2605574920 19.299623434471858 35.29231047643107 chr12 133851895 1978513308 14.781361952327982 34.82695041999203 chr13 115169878 607763633 5.277105815810624 10.689338811585833 chr14 107349540 1255819065 11.698411236787788 23.07486599132711 chr15 102531392 1543398217 15.05293341769904 29.375054788283755 chr16 90354753 2184189478 24.173487342718982 40.74009181023773 chr17 81195210 1699252960 20.927995136658925 39.76082375260481 chr18 78077248 677786919 8.680978599553098 96.69602484714122 chr19 59128983 1870253157 31.630057919311753 59.04245251829293 chr20 63025520 1339282115 21.249838398794648 34.65635036157809 chr21 48129895 555680697 11.545437549780651 24.882528792157473 chr22 51304566 715945058 13.954801956613375 28.9355944502864 chrMT 16571 189369 11.427735200048277 16.77173705677617 chrX 155270560 2587390193 16.663752568419923 27.805388498281157 chrY 59373566 81696726 1.3759780909908628 47.80194932435726