BamQC report ----------------------------------- >>>>>>> Input bam file = SRR611532.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 1,235,385,080 number of mapped reads = 1,220,911,799 (98.83%) number of supplementary alignments = 2,148,935 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 611,950,661 number of mapped paired reads (second in pair) = 608,961,138 number of mapped paired reads (both in pair) = 1,212,733,824 number of mapped paired reads (singletons) = 8,177,975 number of mapped bases = 108,690,886,875 bp number of sequenced bases = 108,664,257,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,487,087 duplication rate = 22.93% >>>>>>> Insert size mean insert size = 29,998.851 std insert size = 1,571,658.7897 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 53.4255 >>>>>>> ACTG content number of A's = 30,974,165,631 bp (28.5%) number of C's = 23,272,193,842 bp (21.42%) number of T's = 30,976,663,005 bp (28.51%) number of G's = 23,434,592,616 bp (21.57%) number of N's = 6,642,814 bp (0.01%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 617,438,710 number of insertions = 9,092,653 mapped reads with insertion percentage = 0.73% number of deletions = 11,093,037 mapped reads with deletion percentage = 0.89% homopolymer indels = 40.56% >>>>>>> Coverage mean coverageData = 35.1103X std coverageData = 308.7805X There is a 91.54% of reference with a coverageData >= 1X There is a 91.43% of reference with a coverageData >= 2X There is a 91.33% of reference with a coverageData >= 3X There is a 91.23% of reference with a coverageData >= 4X There is a 91.09% of reference with a coverageData >= 5X There is a 90.93% of reference with a coverageData >= 6X There is a 90.72% of reference with a coverageData >= 7X There is a 90.45% of reference with a coverageData >= 8X There is a 90.12% of reference with a coverageData >= 9X There is a 89.71% of reference with a coverageData >= 10X There is a 89.21% of reference with a coverageData >= 11X There is a 88.61% of reference with a coverageData >= 12X There is a 87.9% of reference with a coverageData >= 13X There is a 87.07% of reference with a coverageData >= 14X There is a 86.1% of reference with a coverageData >= 15X There is a 85% of reference with a coverageData >= 16X There is a 83.75% of reference with a coverageData >= 17X There is a 82.36% of reference with a coverageData >= 18X There is a 80.81% of reference with a coverageData >= 19X There is a 79.12% of reference with a coverageData >= 20X There is a 77.28% of reference with a coverageData >= 21X There is a 75.31% of reference with a coverageData >= 22X There is a 73.2% of reference with a coverageData >= 23X There is a 70.99% of reference with a coverageData >= 24X There is a 68.68% of reference with a coverageData >= 25X There is a 66.29% of reference with a coverageData >= 26X There is a 63.83% of reference with a coverageData >= 27X There is a 61.32% of reference with a coverageData >= 28X There is a 58.78% of reference with a coverageData >= 29X There is a 56.24% of reference with a coverageData >= 30X There is a 53.69% of reference with a coverageData >= 31X There is a 51.17% of reference with a coverageData >= 32X There is a 48.68% of reference with a coverageData >= 33X There is a 46.23% of reference with a coverageData >= 34X There is a 43.84% of reference with a coverageData >= 35X There is a 41.52% of reference with a coverageData >= 36X There is a 39.26% of reference with a coverageData >= 37X There is a 37.09% of reference with a coverageData >= 38X There is a 35% of reference with a coverageData >= 39X There is a 32.99% of reference with a coverageData >= 40X There is a 31.07% of reference with a coverageData >= 41X There is a 29.23% of reference with a coverageData >= 42X There is a 27.48% of reference with a coverageData >= 43X There is a 25.81% of reference with a coverageData >= 44X There is a 24.23% of reference with a coverageData >= 45X There is a 22.72% of reference with a coverageData >= 46X There is a 21.29% of reference with a coverageData >= 47X There is a 19.94% of reference with a coverageData >= 48X There is a 18.67% of reference with a coverageData >= 49X There is a 17.46% of reference with a coverageData >= 50X There is a 16.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7327130546 29.39663907998849 618.4805698194522 chr2 243199373 10370246707 42.64092698544909 278.914902424532 chr3 198022430 7819344400 39.4871651660875 23.75278850953001 chr4 191154276 5478085485 28.657928034003277 212.13290204072504 chr5 180915260 6645796538 36.73430609446655 35.121941289902594 chr6 171115067 4933767183 28.8330377301024 112.38429545997874 chr7 159138663 8356883095 52.51321669706374 332.15805474158924 chr8 146364022 4560915751 31.16145408329924 200.0809213742899 chr9 141213431 4893438635 34.65278479778598 387.70398431254296 chr10 135534747 4642285182 34.25162391751836 718.1881410909015 chr11 135006516 5945172932 44.03619253458848 184.49400589553466 chr12 133851895 4832105621 36.10039006918804 31.38448049479961 chr13 115169878 4274962987 37.11875935997779 24.78033338299869 chr14 107349540 3277518848 30.531279854575995 39.62932164997203 chr15 102531392 2582723626 25.18958901874657 19.22084681193127 chr16 90354753 2972174162 32.89449711627235 245.37832736511297 chr17 81195210 3914164283 48.20683736146504 219.6318615682217 chr18 78077248 1906805145 24.42203322791295 457.39465852078985 chr19 59128983 2466098043 41.7070938460078 296.19490045513095 chr20 63025520 3452235817 54.77520561512225 112.4830380805173 chr21 48129895 1702798007 35.37921715806777 133.03321867039298 chr22 51304566 1237535260 24.12134740599891 23.916087587245393 chrMT 16571 408804694 24669.88679017561 4951.40652582076 chrX 155270560 4292897219 27.647850429598503 96.6830676782862 chrY 59373566 396996709 6.686421849750443 305.61309393786075