BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438284.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 684,039,712 number of mapped reads = 681,613,601 (99.65%) number of supplementary alignments = 11,360,881 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 341,106,789 number of mapped paired reads (second in pair) = 340,506,812 number of mapped paired reads (both in pair) = 679,838,488 number of mapped paired reads (singletons) = 1,775,113 number of mapped bases = 98,541,338,746 bp number of sequenced bases = 98,512,153,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 295,587,477 duplication rate = 40.73% >>>>>>> Insert size mean insert size = 41,110.5726 std insert size = 1,969,902.2505 median insert size = 269 >>>>>>> Mapping quality mean mapping quality = 55.1655 >>>>>>> ACTG content number of A's = 29,710,796,305 bp (30.16%) number of C's = 19,747,824,220 bp (20.05%) number of T's = 28,245,224,012 bp (28.67%) number of G's = 20,807,572,250 bp (21.12%) number of N's = 736,358 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 504,769,674 number of insertions = 12,908,609 mapped reads with insertion percentage = 1.86% number of deletions = 11,521,768 mapped reads with deletion percentage = 1.66% homopolymer indels = 48.8% >>>>>>> Coverage mean coverageData = 31.8317X std coverageData = 62.8329X There is a 91.54% of reference with a coverageData >= 1X There is a 90.92% of reference with a coverageData >= 2X There is a 90.19% of reference with a coverageData >= 3X There is a 89.38% of reference with a coverageData >= 4X There is a 88.44% of reference with a coverageData >= 5X There is a 87.38% of reference with a coverageData >= 6X There is a 86.2% of reference with a coverageData >= 7X There is a 84.9% of reference with a coverageData >= 8X There is a 83.48% of reference with a coverageData >= 9X There is a 81.96% of reference with a coverageData >= 10X There is a 80.34% of reference with a coverageData >= 11X There is a 78.62% of reference with a coverageData >= 12X There is a 76.83% of reference with a coverageData >= 13X There is a 74.98% of reference with a coverageData >= 14X There is a 73.06% of reference with a coverageData >= 15X There is a 71.11% of reference with a coverageData >= 16X There is a 69.11% of reference with a coverageData >= 17X There is a 67.1% of reference with a coverageData >= 18X There is a 65.07% of reference with a coverageData >= 19X There is a 63.03% of reference with a coverageData >= 20X There is a 61% of reference with a coverageData >= 21X There is a 58.98% of reference with a coverageData >= 22X There is a 56.97% of reference with a coverageData >= 23X There is a 54.99% of reference with a coverageData >= 24X There is a 53.04% of reference with a coverageData >= 25X There is a 51.13% of reference with a coverageData >= 26X There is a 49.25% of reference with a coverageData >= 27X There is a 47.41% of reference with a coverageData >= 28X There is a 45.61% of reference with a coverageData >= 29X There is a 43.86% of reference with a coverageData >= 30X There is a 42.16% of reference with a coverageData >= 31X There is a 40.51% of reference with a coverageData >= 32X There is a 38.9% of reference with a coverageData >= 33X There is a 37.35% of reference with a coverageData >= 34X There is a 35.85% of reference with a coverageData >= 35X There is a 34.4% of reference with a coverageData >= 36X There is a 33% of reference with a coverageData >= 37X There is a 31.64% of reference with a coverageData >= 38X There is a 30.34% of reference with a coverageData >= 39X There is a 29.09% of reference with a coverageData >= 40X There is a 27.88% of reference with a coverageData >= 41X There is a 26.72% of reference with a coverageData >= 42X There is a 25.61% of reference with a coverageData >= 43X There is a 24.54% of reference with a coverageData >= 44X There is a 23.51% of reference with a coverageData >= 45X There is a 22.52% of reference with a coverageData >= 46X There is a 21.58% of reference with a coverageData >= 47X There is a 20.67% of reference with a coverageData >= 48X There is a 19.8% of reference with a coverageData >= 49X There is a 18.96% of reference with a coverageData >= 50X There is a 18.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8254948405 33.119068557907426 31.914389112040617 chr2 243199373 8632627927 35.49609450267785 80.28170341123862 chr3 198022430 7000282622 35.35095808085983 34.9870588387277 chr4 191154276 6352360266 33.231588635767686 24.09877794027499 chr5 180915260 6204804418 34.296744332125435 26.07780216712422 chr6 171115067 5829234857 34.06616938647489 26.427128282440137 chr7 159138663 5242094563 32.940421040234575 26.208478987738463 chr8 146364022 5015346053 34.2662492084291 25.845068065511825 chr9 141213431 4160213167 29.460463764243503 31.900133660078332 chr10 135534747 4628208262 34.147761842946444 36.141743981926794 chr11 135006516 4644712111 34.40361434851041 28.20258010751321 chr12 133851895 4815305259 35.97487550699226 28.523004411470172 chr13 115169878 3196414228 27.75390825715731 24.997724697228374 chr14 107349540 3212268091 29.92344532636097 28.998829934264684 chr15 102531392 3035494780 29.60551613304928 30.374043073276596 chr16 90354753 2837358427 31.402425802658108 47.7638981002918 chr17 81195210 2757253641 33.958328834915264 38.145446219359975 chr18 78077248 2507891043 32.12063830682147 25.623070876404636 chr19 59128983 1709095310 28.904527412555023 41.331419249796284 chr20 63025520 2284757203 36.25130269452755 31.763890357476246 chr21 48129895 1323639421 27.50139847593684 34.683110508115014 chr22 51304566 1215928103 23.700192746976946 31.301578505108665 chrMT 16571 338820906 20446.61794701587 8115.243638307759 chrX 155270560 2877798453 18.534089482256004 16.361997228714245 chrY 59373566 464481230 7.823030706964779 23.287897249405557