BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630498.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 = 99,433,784 number of mapped reads = 99,091,196 (99.66%) number of supplementary alignments = 589,228 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 49,661,406 number of mapped paired reads (second in pair) = 49,429,790 number of mapped paired reads (both in pair) = 98,825,300 number of mapped paired reads (singletons) = 265,896 number of mapped bases = 9,841,733,002 bp number of sequenced bases = 9,839,635,268 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,123,717 duplication rate = 15.56% >>>>>>> Insert size mean insert size = 49,079.993 std insert size = 2,100,549.8053 median insert size = 316 >>>>>>> Mapping quality mean mapping quality = 53.7019 >>>>>>> ACTG content number of A's = 3,065,070,486 bp (31.15%) number of C's = 1,839,343,541 bp (18.69%) number of T's = 3,048,655,520 bp (30.98%) number of G's = 1,855,212,650 bp (18.85%) number of N's = 31,353,071 bp (0.32%) GC percentage = 37.55% >>>>>>> Mismatches and indels general error rate = 0.0125 number of mismatches = 121,297,799 number of insertions = 872,881 mapped reads with insertion percentage = 0.87% number of deletions = 944,391 mapped reads with deletion percentage = 0.93% homopolymer indels = 43.91% >>>>>>> Coverage mean coverageData = 3.1792X std coverageData = 12.2427X There is a 36.17% of reference with a coverageData >= 1X There is a 25.26% of reference with a coverageData >= 2X There is a 19.88% of reference with a coverageData >= 3X There is a 16.48% of reference with a coverageData >= 4X There is a 14.08% of reference with a coverageData >= 5X There is a 12.27% of reference with a coverageData >= 6X There is a 10.85% of reference with a coverageData >= 7X There is a 9.7% of reference with a coverageData >= 8X There is a 8.76% of reference with a coverageData >= 9X There is a 7.96% of reference with a coverageData >= 10X There is a 7.28% of reference with a coverageData >= 11X There is a 6.69% of reference with a coverageData >= 12X There is a 6.18% of reference with a coverageData >= 13X There is a 5.73% of reference with a coverageData >= 14X There is a 5.32% of reference with a coverageData >= 15X There is a 4.97% of reference with a coverageData >= 16X There is a 4.65% of reference with a coverageData >= 17X There is a 4.36% of reference with a coverageData >= 18X There is a 4.09% of reference with a coverageData >= 19X There is a 3.85% of reference with a coverageData >= 20X There is a 3.64% of reference with a coverageData >= 21X There is a 3.44% of reference with a coverageData >= 22X There is a 3.25% of reference with a coverageData >= 23X There is a 3.08% of reference with a coverageData >= 24X There is a 2.93% of reference with a coverageData >= 25X There is a 2.78% of reference with a coverageData >= 26X There is a 2.65% of reference with a coverageData >= 27X There is a 2.52% of reference with a coverageData >= 28X There is a 2.4% of reference with a coverageData >= 29X There is a 2.3% of reference with a coverageData >= 30X There is a 2.19% of reference with a coverageData >= 31X There is a 2.1% of reference with a coverageData >= 32X There is a 2.01% of reference with a coverageData >= 33X There is a 1.92% of reference with a coverageData >= 34X There is a 1.84% of reference with a coverageData >= 35X There is a 1.77% of reference with a coverageData >= 36X There is a 1.7% of reference with a coverageData >= 37X There is a 1.63% of reference with a coverageData >= 38X There is a 1.57% of reference with a coverageData >= 39X There is a 1.51% of reference with a coverageData >= 40X There is a 1.45% of reference with a coverageData >= 41X There is a 1.4% of reference with a coverageData >= 42X There is a 1.35% of reference with a coverageData >= 43X There is a 1.3% of reference with a coverageData >= 44X There is a 1.26% of reference with a coverageData >= 45X There is a 1.21% of reference with a coverageData >= 46X There is a 1.17% of reference with a coverageData >= 47X There is a 1.13% of reference with a coverageData >= 48X There is a 1.1% of reference with a coverageData >= 49X There is a 1.06% of reference with a coverageData >= 50X There is a 1.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 842275728 3.379232214631072 13.65810368089501 chr2 243199373 841842187 3.461531074753223 13.393415985516533 chr3 198022430 716931353 3.6204552837777015 12.511128488424054 chr4 191154276 736521389 3.8530207349376795 13.609990683417184 chr5 180915260 622725393 3.4420832880543077 12.748359890694442 chr6 171115067 708038468 4.137791489746488 14.08139960423892 chr7 159138663 496189574 3.117969980682821 10.953518016778878 chr8 146364022 544259662 3.7185344770041917 14.757471773943605 chr9 141213431 368495976 2.609496656164384 10.85119494278699 chr10 135534747 389442337 2.8733763527075458 9.202728249270805 chr11 135006516 473408752 3.506562246225212 12.745818448233905 chr12 133851895 443226464 3.311320052659695 11.42621500582642 chr13 115169878 328539556 2.852651767157381 10.677980813396399 chr14 107349540 313256162 2.918095056578724 11.04796238312564 chr15 102531392 229900696 2.242246901319744 9.197150855757567 chr16 90354753 180883602 2.001926805112289 7.541136635993164 chr17 81195210 159415286 1.96335825721739 7.864458710681274 chr18 78077248 296426469 3.7965793697031947 14.502294627835926 chr19 59128983 70166342 1.186665801439541 4.85832029775582 chr20 63025520 150382824 2.386062407735787 9.48137941551512 chr21 48129895 90560588 1.8815870676634554 6.94384857548579 chr22 51304566 44703293 0.871331666659065 4.958832286965609 chrMT 16571 4159 0.2509806288093658 0.8707135172570487 chrX 155270560 785477445 5.058766098351162 18.03907569691279 chrY 59373566 8659297 0.14584431394940975 2.736457356139193