BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6432722.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP127755/SRP127755.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 = 373,729,990 number of mapped reads = 373,591,062 (99.96%) number of supplementary alignments = 2,837,477 (0.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 186,799,832 number of mapped paired reads (second in pair) = 186,791,230 number of mapped paired reads (both in pair) = 373,539,690 number of mapped paired reads (singletons) = 51,372 number of mapped bases = 51,238,306,668 bp number of sequenced bases = 51,188,778,418 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 190,052,382 duplication rate = 32.27% >>>>>>> Insert size mean insert size = 74,905.0434 std insert size = 2,789,069.5772 median insert size = 317 >>>>>>> Mapping quality mean mapping quality = 57.4236 >>>>>>> ACTG content number of A's = 14,134,346,348 bp (27.61%) number of C's = 10,838,130,955 bp (21.17%) number of T's = 13,932,782,397 bp (27.22%) number of G's = 12,274,211,192 bp (23.98%) number of N's = 9,307,526 bp (0.02%) GC percentage = 45.15% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 456,436,237 number of insertions = 10,635,356 mapped reads with insertion percentage = 2.79% number of deletions = 34,716,048 mapped reads with deletion percentage = 8.87% homopolymer indels = 52.35% >>>>>>> Coverage mean coverageData = 16.5515X std coverageData = 47.394X There is a 56.88% of reference with a coverageData >= 1X There is a 49.11% of reference with a coverageData >= 2X There is a 44.03% of reference with a coverageData >= 3X There is a 40.26% of reference with a coverageData >= 4X There is a 37.24% of reference with a coverageData >= 5X There is a 34.72% of reference with a coverageData >= 6X There is a 32.57% of reference with a coverageData >= 7X There is a 30.7% of reference with a coverageData >= 8X There is a 29.06% of reference with a coverageData >= 9X There is a 27.6% of reference with a coverageData >= 10X There is a 26.3% of reference with a coverageData >= 11X There is a 25.11% of reference with a coverageData >= 12X There is a 24.04% of reference with a coverageData >= 13X There is a 23.05% of reference with a coverageData >= 14X There is a 22.14% of reference with a coverageData >= 15X There is a 21.3% of reference with a coverageData >= 16X There is a 20.51% of reference with a coverageData >= 17X There is a 19.79% of reference with a coverageData >= 18X There is a 19.11% of reference with a coverageData >= 19X There is a 18.47% of reference with a coverageData >= 20X There is a 17.87% of reference with a coverageData >= 21X There is a 17.31% of reference with a coverageData >= 22X There is a 16.78% of reference with a coverageData >= 23X There is a 16.27% of reference with a coverageData >= 24X There is a 15.8% of reference with a coverageData >= 25X There is a 15.35% of reference with a coverageData >= 26X There is a 14.92% of reference with a coverageData >= 27X There is a 14.51% of reference with a coverageData >= 28X There is a 14.12% of reference with a coverageData >= 29X There is a 13.75% of reference with a coverageData >= 30X There is a 13.39% of reference with a coverageData >= 31X There is a 13.05% of reference with a coverageData >= 32X There is a 12.73% of reference with a coverageData >= 33X There is a 12.41% of reference with a coverageData >= 34X There is a 12.11% of reference with a coverageData >= 35X There is a 11.83% of reference with a coverageData >= 36X There is a 11.55% of reference with a coverageData >= 37X There is a 11.29% of reference with a coverageData >= 38X There is a 11.03% of reference with a coverageData >= 39X There is a 10.78% of reference with a coverageData >= 40X There is a 10.55% of reference with a coverageData >= 41X There is a 10.32% of reference with a coverageData >= 42X There is a 10.1% of reference with a coverageData >= 43X There is a 9.88% of reference with a coverageData >= 44X There is a 9.68% of reference with a coverageData >= 45X There is a 9.48% of reference with a coverageData >= 46X There is a 9.29% of reference with a coverageData >= 47X There is a 9.1% of reference with a coverageData >= 48X There is a 8.92% of reference with a coverageData >= 49X There is a 8.74% of reference with a coverageData >= 50X There is a 8.57% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4543287010 18.227786120540898 52.23294326909299 chr2 243199373 4137488215 17.012742113442865 48.75150525296481 chr3 198022430 4215160525 21.286278150409526 54.207045957483324 chr4 191154276 2144267957 11.217473141955768 33.539768970697395 chr5 180915260 2521602580 13.938031429742301 39.75709496968938 chr6 171115067 2333620521 13.637726717542646 40.685897332682124 chr7 159138663 2824832697 17.7507630373896 47.663445221442416 chr8 146364022 1857725054 12.692497982871775 35.63113926973935 chr9 141213431 2160625352 15.300423881068367 46.22975433405333 chr10 135534747 2162193759 15.953058583567504 42.20501857392491 chr11 135006516 3289212160 24.363358580411038 61.407230831808896 chr12 133851895 2898333206 21.653284819015823 55.7521159092559 chr13 115169878 1551644922 13.472662721757855 41.00369120991976 chr14 107349540 1604589859 14.94733800442927 43.73354259605505 chr15 102531392 1907114690 18.6003003841009 52.34357121962339 chr16 90354753 1994859676 22.07808233397528 60.826491724668344 chr17 81195210 1783627897 21.967156646309554 55.429266747180385 chr18 78077248 1070423167 13.709796316079172 38.821094557701045 chr19 59128983 1323747403 22.387454270945266 58.31027366198427 chr20 63025520 1700110930 26.97496077779287 63.852032491877466 chr21 48129895 579313005 12.036448552401787 39.11614797667526 chr22 51304566 1080955201 21.0693761837884 60.06338641863813 chrMT 16571 7637461 460.89318689276445 634.8582336600053 chrX 155270560 1453361189 9.360185143919105 28.493806455713557 chrY 59373566 92572232 1.5591489316979883 14.3295445945256