BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153385.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 = 83,747,320 number of mapped reads = 83,156,296 (99.29%) number of supplementary alignments = 415,604 (0.5%) number of secondary alignments = 0 number of mapped bases = 8,009,579,506 bp number of sequenced bases = 8,008,750,330 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,336,500 duplication rate = 46.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4135 >>>>>>> ACTG content number of A's = 1,981,855,547 bp (24.75%) number of C's = 2,022,464,575 bp (25.25%) number of T's = 1,969,121,728 bp (24.59%) number of G's = 2,034,235,089 bp (25.4%) number of N's = 1,073,391 bp (0.01%) GC percentage = 50.65% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 22,217,570 number of insertions = 544,398 mapped reads with insertion percentage = 0.65% number of deletions = 360,916 mapped reads with deletion percentage = 0.43% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 2.5873X std coverageData = 40.6678X There is a 8.74% of reference with a coverageData >= 1X There is a 6.11% of reference with a coverageData >= 2X There is a 4.31% of reference with a coverageData >= 3X There is a 3.81% of reference with a coverageData >= 4X There is a 3.38% of reference with a coverageData >= 5X There is a 3.14% of reference with a coverageData >= 6X There is a 2.93% of reference with a coverageData >= 7X There is a 2.77% of reference with a coverageData >= 8X There is a 2.64% of reference with a coverageData >= 9X There is a 2.52% of reference with a coverageData >= 10X There is a 2.42% of reference with a coverageData >= 11X There is a 2.32% of reference with a coverageData >= 12X There is a 2.24% of reference with a coverageData >= 13X There is a 2.16% of reference with a coverageData >= 14X There is a 2.09% of reference with a coverageData >= 15X There is a 2.03% of reference with a coverageData >= 16X There is a 1.96% of reference with a coverageData >= 17X There is a 1.91% of reference with a coverageData >= 18X There is a 1.85% of reference with a coverageData >= 19X There is a 1.8% of reference with a coverageData >= 20X There is a 1.76% of reference with a coverageData >= 21X There is a 1.71% of reference with a coverageData >= 22X There is a 1.67% of reference with a coverageData >= 23X There is a 1.63% of reference with a coverageData >= 24X There is a 1.59% of reference with a coverageData >= 25X There is a 1.56% of reference with a coverageData >= 26X There is a 1.52% of reference with a coverageData >= 27X There is a 1.49% of reference with a coverageData >= 28X There is a 1.46% of reference with a coverageData >= 29X There is a 1.43% of reference with a coverageData >= 30X There is a 1.4% of reference with a coverageData >= 31X There is a 1.37% of reference with a coverageData >= 32X There is a 1.34% of reference with a coverageData >= 33X There is a 1.32% of reference with a coverageData >= 34X There is a 1.29% of reference with a coverageData >= 35X There is a 1.27% of reference with a coverageData >= 36X There is a 1.25% of reference with a coverageData >= 37X There is a 1.22% of reference with a coverageData >= 38X There is a 1.2% of reference with a coverageData >= 39X There is a 1.18% of reference with a coverageData >= 40X There is a 1.16% of reference with a coverageData >= 41X There is a 1.14% of reference with a coverageData >= 42X There is a 1.12% of reference with a coverageData >= 43X There is a 1.1% of reference with a coverageData >= 44X There is a 1.09% of reference with a coverageData >= 45X There is a 1.07% of reference with a coverageData >= 46X There is a 1.05% of reference with a coverageData >= 47X There is a 1.03% of reference with a coverageData >= 48X There is a 1.02% of reference with a coverageData >= 49X There is a 1% of reference with a coverageData >= 50X There is a 0.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1088887640 4.3686456452198765 59.1567807678372 chr2 243199373 503042469 2.068436537457685 33.97275804820958 chr3 198022430 372910638 1.8831737293598507 28.9399559183901 chr4 191154276 275038826 1.4388316691382828 25.790547824576752 chr5 180915260 414676968 2.2921060832568796 43.5182494934464 chr6 171115067 489542976 2.860899303507855 55.18328182999829 chr7 159138663 427031001 2.6833893973333183 39.01048932750512 chr8 146364022 357852009 2.444945172386695 45.61976217525972 chr9 141213431 363439392 2.5736885608281836 45.792981978050584 chr10 135534747 256687804 1.8938892769689533 26.21807033571989 chr11 135006516 386218403 2.8607389809244466 34.489196880646105 chr12 133851895 371951586 2.7788294368189557 34.8419168389366 chr13 115169878 129228023 1.1220644255609962 20.684244595926387 chr14 107349540 223799114 2.08477012570338 37.48602954082017 chr15 102531392 347772710 3.3918656834386876 39.25149110429252 chr16 90354753 326993450 3.6189955607537327 49.916865090258646 chr17 81195210 398502795 4.907959410413496 51.36667942179622 chr18 78077248 132230684 1.6935879194922443 28.787954130245275 chr19 59128983 374502806 6.333658842060585 72.66061201920377 chr20 63025520 141679570 2.2479714566416904 30.03192047429242 chr21 48129895 88247135 1.833520206100595 33.99118333195062 chr22 51304566 140275061 2.734163290651362 31.576056570145386 chrMT 16571 4192 0.2529720596222316 0.8281722995107248 chrX 155270560 392288150 2.526481195147361 36.48641323195753 chrY 59373566 6776104 0.11412661318001348 7.01252586001681