BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630496.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 77,153,952 number of mapped reads = 76,860,749 (99.62%) number of supplementary alignments = 437,128 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 38,516,061 number of mapped paired reads (second in pair) = 38,344,688 number of mapped paired reads (both in pair) = 76,657,942 number of mapped paired reads (singletons) = 202,807 number of mapped bases = 7,638,414,257 bp number of sequenced bases = 7,636,800,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,922,365 duplication rate = 15.19% >>>>>>> Insert size mean insert size = 41,207.1182 std insert size = 1,897,800.7043 median insert size = 323 >>>>>>> Mapping quality mean mapping quality = 53.8451 >>>>>>> ACTG content number of A's = 2,384,597,436 bp (31.23%) number of C's = 1,421,540,279 bp (18.61%) number of T's = 2,373,213,895 bp (31.08%) number of G's = 1,433,053,297 bp (18.77%) number of N's = 24,395,698 bp (0.32%) GC percentage = 37.38% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 93,112,007 number of insertions = 668,737 mapped reads with insertion percentage = 0.86% number of deletions = 724,046 mapped reads with deletion percentage = 0.92% homopolymer indels = 43.83% >>>>>>> Coverage mean coverageData = 2.4674X std coverageData = 11.0066X There is a 30.39% of reference with a coverageData >= 1X There is a 20.4% of reference with a coverageData >= 2X There is a 15.72% of reference with a coverageData >= 3X There is a 12.86% of reference with a coverageData >= 4X There is a 10.88% of reference with a coverageData >= 5X There is a 9.42% of reference with a coverageData >= 6X There is a 8.29% of reference with a coverageData >= 7X There is a 7.38% of reference with a coverageData >= 8X There is a 6.64% of reference with a coverageData >= 9X There is a 6.02% of reference with a coverageData >= 10X There is a 5.5% of reference with a coverageData >= 11X There is a 5.05% of reference with a coverageData >= 12X There is a 4.65% of reference with a coverageData >= 13X There is a 4.31% of reference with a coverageData >= 14X There is a 4.01% of reference with a coverageData >= 15X There is a 3.74% of reference with a coverageData >= 16X There is a 3.5% of reference with a coverageData >= 17X There is a 3.28% of reference with a coverageData >= 18X There is a 3.08% of reference with a coverageData >= 19X There is a 2.9% of reference with a coverageData >= 20X There is a 2.74% of reference with a coverageData >= 21X There is a 2.59% of reference with a coverageData >= 22X There is a 2.45% of reference with a coverageData >= 23X There is a 2.33% of reference with a coverageData >= 24X There is a 2.21% of reference with a coverageData >= 25X There is a 2.1% of reference with a coverageData >= 26X There is a 2% of reference with a coverageData >= 27X There is a 1.91% of reference with a coverageData >= 28X There is a 1.82% of reference with a coverageData >= 29X There is a 1.74% of reference with a coverageData >= 30X There is a 1.66% of reference with a coverageData >= 31X There is a 1.59% of reference with a coverageData >= 32X There is a 1.52% of reference with a coverageData >= 33X There is a 1.46% of reference with a coverageData >= 34X There is a 1.4% of reference with a coverageData >= 35X There is a 1.34% of reference with a coverageData >= 36X There is a 1.29% of reference with a coverageData >= 37X There is a 1.23% of reference with a coverageData >= 38X There is a 1.19% of reference with a coverageData >= 39X There is a 1.14% of reference with a coverageData >= 40X There is a 1.1% of reference with a coverageData >= 41X There is a 1.06% of reference with a coverageData >= 42X There is a 1.02% of reference with a coverageData >= 43X There is a 0.98% of reference with a coverageData >= 44X There is a 0.94% of reference with a coverageData >= 45X There is a 0.91% of reference with a coverageData >= 46X There is a 0.88% of reference with a coverageData >= 47X There is a 0.85% of reference with a coverageData >= 48X There is a 0.82% of reference with a coverageData >= 49X There is a 0.79% of reference with a coverageData >= 50X There is a 0.77% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 523203488 2.0991060559885226 9.47598952917976 chr2 243199373 630583180 2.592865155125215 10.092583103084413 chr3 198022430 592417211 2.991667211638601 11.200094003828704 chr4 191154276 644495003 3.371596055742954 12.408545944372861 chr5 180915260 536914708 2.9677690428104295 12.701726725897682 chr6 171115067 527854983 3.084795466900644 13.302630945647467 chr7 159138663 349087078 2.193603184915535 9.991439214535156 chr8 146364022 413701617 2.8265253396767136 10.511051615293272 chr9 141213431 315058560 2.23108069656632 8.915358627273271 chr10 135534747 329413877 2.430475463240434 9.736351077027003 chr11 135006516 366923363 2.7178196569415953 10.556917881126607 chr12 133851895 381548523 2.850527614868658 11.138442095195701 chr13 115169878 265811902 2.3079984681411227 9.11976825516911 chr14 107349540 229148271 2.134599468241783 13.202978696500145 chr15 102531392 209003495 2.038434189989345 8.906807441591932 chr16 90354753 125238052 1.3860704372685297 12.017271630620728 chr17 81195210 107224987 1.3205826673765608 6.734013821130089 chr18 78077248 151032254 1.9343952030686327 6.894735150057943 chr19 59128983 38261689 0.6470885690694189 2.892796905000877 chr20 63025520 155798450 2.4719899177349114 19.056347138435722 chr21 48129895 97614651 2.0281500925775964 9.02743536493707 chr22 51304566 35941371 0.7005491674951504 3.5340606818327553 chrMT 16571 573 0.034578480477943395 0.33423408135392674 chrX 155270560 608208617 3.917089092742372 16.002822507136255 chrY 59373566 3928354 0.06616334952830692 0.9071837490153262