BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777276.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 60,091,208 number of mapped reads = 58,405,595 (97.19%) number of supplementary alignments = 199,590 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,204,052 number of mapped paired reads (second in pair) = 29,201,543 number of mapped paired reads (both in pair) = 58,365,622 number of mapped paired reads (singletons) = 39,973 number of mapped bases = 5,806,159,896 bp number of sequenced bases = 5,803,215,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,979,460 duplication rate = 45.06% >>>>>>> Insert size mean insert size = 96,283.1054 std insert size = 3,202,604.7949 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 55.1229 >>>>>>> ACTG content number of A's = 1,389,850,463 bp (23.95%) number of C's = 1,496,537,805 bp (25.79%) number of T's = 1,393,158,432 bp (24.01%) number of G's = 1,523,431,645 bp (26.25%) number of N's = 237,128 bp (0%) GC percentage = 52.04% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 36,131,278 number of insertions = 601,198 mapped reads with insertion percentage = 1.02% number of deletions = 2,329,987 mapped reads with deletion percentage = 3.91% homopolymer indels = 55.39% >>>>>>> Coverage mean coverageData = 1.8756X std coverageData = 27.6997X There is a 11.55% of reference with a coverageData >= 1X There is a 6.53% of reference with a coverageData >= 2X There is a 4.36% of reference with a coverageData >= 3X There is a 3.44% of reference with a coverageData >= 4X There is a 2.87% of reference with a coverageData >= 5X There is a 2.53% of reference with a coverageData >= 6X There is a 2.29% of reference with a coverageData >= 7X There is a 2.11% of reference with a coverageData >= 8X There is a 1.97% of reference with a coverageData >= 9X There is a 1.85% of reference with a coverageData >= 10X There is a 1.76% of reference with a coverageData >= 11X There is a 1.68% of reference with a coverageData >= 12X There is a 1.6% of reference with a coverageData >= 13X There is a 1.54% of reference with a coverageData >= 14X There is a 1.48% of reference with a coverageData >= 15X There is a 1.43% of reference with a coverageData >= 16X There is a 1.39% of reference with a coverageData >= 17X There is a 1.34% of reference with a coverageData >= 18X There is a 1.3% of reference with a coverageData >= 19X There is a 1.27% of reference with a coverageData >= 20X There is a 1.23% of reference with a coverageData >= 21X There is a 1.2% of reference with a coverageData >= 22X There is a 1.17% of reference with a coverageData >= 23X There is a 1.14% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.09% of reference with a coverageData >= 26X There is a 1.06% of reference with a coverageData >= 27X There is a 1.04% of reference with a coverageData >= 28X There is a 1.02% of reference with a coverageData >= 29X There is a 1% of reference with a coverageData >= 30X There is a 0.98% of reference with a coverageData >= 31X There is a 0.96% of reference with a coverageData >= 32X There is a 0.94% of reference with a coverageData >= 33X There is a 0.92% of reference with a coverageData >= 34X There is a 0.91% of reference with a coverageData >= 35X There is a 0.89% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.86% of reference with a coverageData >= 38X There is a 0.84% of reference with a coverageData >= 39X There is a 0.83% of reference with a coverageData >= 40X There is a 0.82% of reference with a coverageData >= 41X There is a 0.8% of reference with a coverageData >= 42X There is a 0.79% of reference with a coverageData >= 43X There is a 0.78% of reference with a coverageData >= 44X There is a 0.77% of reference with a coverageData >= 45X There is a 0.75% of reference with a coverageData >= 46X There is a 0.74% of reference with a coverageData >= 47X There is a 0.73% of reference with a coverageData >= 48X There is a 0.72% of reference with a coverageData >= 49X There is a 0.71% of reference with a coverageData >= 50X There is a 0.7% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 669809034 2.687291334772642 32.93712666785305 chr2 243199373 407884983 1.6771629711397322 25.015927034201777 chr3 198022430 317165433 1.601664180163833 25.2578604057001 chr4 191154276 140639964 0.7357406119442497 15.546313636988147 chr5 180915260 221460006 1.224109044201136 18.809382473454757 chr6 171115067 281243648 1.6435937111253913 27.155022072395646 chr7 159138663 325859092 2.047642514126187 32.2173756492398 chr8 146364022 132105207 0.9025797815258179 17.245407362642574 chr9 141213431 227659079 1.6121630739217716 23.482417907802255 chr10 135534747 224118692 1.6535884484293906 23.975597521607057 chr11 135006516 393511654 2.9147604549694477 34.662468524347744 chr12 133851895 339181586 2.534006604837384 34.62963639973567 chr13 115169878 92131507 0.7999618355070238 14.89933319008729 chr14 107349540 128060039 1.1929258290254434 18.19240741077867 chr15 102531392 280228619 2.733100697589281 34.882865761169455 chr16 90354753 270270721 2.991217528977142 34.698334998195925 chr17 81195210 399686513 4.922538078293043 50.55779502269593 chr18 78077248 52220670 0.6688333840864883 12.196946996777896 chr19 59128983 348046672 5.886227943409748 51.50999811063417 chr20 63025520 229413753 3.640013648439553 43.62033825977855 chr21 48129895 42375551 0.8804413764044156 15.31895004877525 chr22 51304566 137237804 2.674962770370185 31.13107752722441 chrMT 16571 59095 3.566169814736588 4.3767905561503895 chrX 155270560 144793460 0.932523589790621 17.463706664272443 chrY 59373566 997114 0.016793904546679915 0.9022963170361