BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124847.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 100,061,340 number of mapped reads = 96,584,022 (96.52%) number of supplementary alignments = 3,011,773 (3.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 49,652,754 number of mapped paired reads (second in pair) = 46,931,268 number of mapped paired reads (both in pair) = 93,663,754 number of mapped paired reads (singletons) = 2,920,268 number of mapped bases = 12,638,519,044 bp number of sequenced bases = 12,627,264,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,691,541 duplication rate = 21.17% >>>>>>> Insert size mean insert size = 177,686.2243 std insert size = 4,017,976.1184 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 53.1889 >>>>>>> ACTG content number of A's = 3,633,991,813 bp (28.78%) number of C's = 2,422,668,640 bp (19.19%) number of T's = 3,755,232,619 bp (29.74%) number of G's = 2,815,152,313 bp (22.29%) number of N's = 218,681 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 156,011,990 number of insertions = 2,796,101 mapped reads with insertion percentage = 2.65% number of deletions = 4,882,230 mapped reads with deletion percentage = 4.81% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 4.0826X std coverageData = 57.417X There is a 63.45% of reference with a coverageData >= 1X There is a 50.29% of reference with a coverageData >= 2X There is a 40.06% of reference with a coverageData >= 3X There is a 32.61% of reference with a coverageData >= 4X There is a 26.74% of reference with a coverageData >= 5X There is a 22.18% of reference with a coverageData >= 6X There is a 18.53% of reference with a coverageData >= 7X There is a 15.61% of reference with a coverageData >= 8X There is a 13.23% of reference with a coverageData >= 9X There is a 11.29% of reference with a coverageData >= 10X There is a 9.68% of reference with a coverageData >= 11X There is a 8.35% of reference with a coverageData >= 12X There is a 7.23% of reference with a coverageData >= 13X There is a 6.29% of reference with a coverageData >= 14X There is a 5.5% of reference with a coverageData >= 15X There is a 4.82% of reference with a coverageData >= 16X There is a 4.24% of reference with a coverageData >= 17X There is a 3.75% of reference with a coverageData >= 18X There is a 3.32% of reference with a coverageData >= 19X There is a 2.95% of reference with a coverageData >= 20X There is a 2.63% of reference with a coverageData >= 21X There is a 2.35% of reference with a coverageData >= 22X There is a 2.1% of reference with a coverageData >= 23X There is a 1.89% of reference with a coverageData >= 24X There is a 1.7% of reference with a coverageData >= 25X There is a 1.53% of reference with a coverageData >= 26X There is a 1.39% of reference with a coverageData >= 27X There is a 1.26% of reference with a coverageData >= 28X There is a 1.14% of reference with a coverageData >= 29X There is a 1.04% of reference with a coverageData >= 30X There is a 0.95% of reference with a coverageData >= 31X There is a 0.86% of reference with a coverageData >= 32X There is a 0.79% of reference with a coverageData >= 33X There is a 0.72% of reference with a coverageData >= 34X There is a 0.66% of reference with a coverageData >= 35X There is a 0.61% of reference with a coverageData >= 36X There is a 0.56% of reference with a coverageData >= 37X There is a 0.52% of reference with a coverageData >= 38X There is a 0.48% of reference with a coverageData >= 39X There is a 0.44% of reference with a coverageData >= 40X There is a 0.41% of reference with a coverageData >= 41X There is a 0.38% of reference with a coverageData >= 42X There is a 0.35% of reference with a coverageData >= 43X There is a 0.33% of reference with a coverageData >= 44X There is a 0.31% of reference with a coverageData >= 45X There is a 0.29% of reference with a coverageData >= 46X There is a 0.27% of reference with a coverageData >= 47X There is a 0.25% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.22% of reference with a coverageData >= 50X There is a 0.21% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1027762256 4.123409008477456 24.147681694302122 chr2 243199373 1117236219 4.593910770485416 61.27516839390228 chr3 198022430 886502707 4.476779256774094 8.173574535538163 chr4 191154276 774511591 4.051761787426613 98.21648802694163 chr5 180915260 706057081 3.9026950020689246 8.001975900961886 chr6 171115067 714166376 4.173603111174307 14.283020741012088 chr7 159138663 787159434 4.946374558896476 25.291496480406042 chr8 146364022 731474267 4.997637103741246 11.742055545255981 chr9 141213431 529760423 3.751487512544044 51.318468703849035 chr10 135534747 726383140 5.359386844172144 183.02692397943605 chr11 135006516 495985520 3.673789493241941 12.86059461317467 chr12 133851895 592067806 4.4233053704618825 23.816837457947486 chr13 115169878 332256516 2.8849254837276117 5.398292096052414 chr14 107349540 397193345 3.7000004378220903 8.242074124882985 chr15 102531392 325176138 3.171478818896753 11.628917809367355 chr16 90354753 451442697 4.996335909412536 78.25086570081424 chr17 81195210 287210939 3.5372891947690017 31.562036562099998 chr18 78077248 257571535 3.2989320397153343 42.173306612288094 chr19 59128983 199790534 3.3788934607584915 14.045405803716584 chr20 63025520 260523925 4.133625950249994 32.803152559725056 chr21 48129895 149367593 3.103426529395088 47.39237181632634 chr22 51304566 118532983 2.3103788267110574 7.792011497367733 chrMT 16571 5234622 315.89053165168065 167.629141546046 chrX 155270560 512117821 3.2982287241058446 9.275729625949582 chrY 59373566 253033576 4.261721049397639 136.48762502362877