BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514761.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 21,242,205 number of mapped reads = 17,269,163 (81.3%) number of supplementary alignments = 2,813,666 (13.25%) number of secondary alignments = 0 number of mapped bases = 1,581,449,402 bp number of sequenced bases = 1,579,719,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,335,927 duplication rate = 35.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4622 >>>>>>> ACTG content number of A's = 479,734,188 bp (30.37%) number of C's = 294,852,824 bp (18.66%) number of T's = 485,250,072 bp (30.72%) number of G's = 319,777,627 bp (20.24%) number of N's = 104,687 bp (0.01%) GC percentage = 38.91% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 9,911,268 number of insertions = 1,119,800 mapped reads with insertion percentage = 6.16% number of deletions = 553,573 mapped reads with deletion percentage = 2.97% homopolymer indels = 40.16% >>>>>>> Coverage mean coverageData = 0.5109X std coverageData = 70.5532X There is a 2.78% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 1.42% of reference with a coverageData >= 3X There is a 1.22% of reference with a coverageData >= 4X There is a 1.08% of reference with a coverageData >= 5X There is a 0.97% of reference with a coverageData >= 6X There is a 0.89% of reference with a coverageData >= 7X There is a 0.82% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.71% of reference with a coverageData >= 10X There is a 0.67% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.6% of reference with a coverageData >= 13X There is a 0.57% of reference with a coverageData >= 14X There is a 0.54% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.49% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.45% of reference with a coverageData >= 19X There is a 0.43% of reference with a coverageData >= 20X There is a 0.42% of reference with a coverageData >= 21X There is a 0.4% of reference with a coverageData >= 22X There is a 0.39% of reference with a coverageData >= 23X There is a 0.37% of reference with a coverageData >= 24X There is a 0.36% of reference with a coverageData >= 25X There is a 0.35% of reference with a coverageData >= 26X There is a 0.34% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.32% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.28% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.25% of reference with a coverageData >= 37X There is a 0.25% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.2% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 90301268 0.36229104520465766 9.590549263247466 chr2 243199373 122617245 0.5041840506718741 9.349389668508184 chr3 198022430 71074097 0.35891942645083186 8.814593096170778 chr4 191154276 101040826 0.5285826093683617 9.965699910004545 chr5 180915260 75393908 0.4167360343179453 13.940214684813395 chr6 171115067 127106839 0.7428150029593829 122.48111435407202 chr7 159138663 86424946 0.5430795029363794 10.45832965263561 chr8 146364022 90416053 0.6177478028036152 22.335355597648924 chr9 141213431 149595847 1.0593599060701244 121.41841892316774 chr10 135534747 57476242 0.42407016113735024 10.468635664338477 chr11 135006516 49044713 0.3632766362180622 15.203709838195556 chr12 133851895 62882063 0.4697883657157039 8.344533641026606 chr13 115169878 63546394 0.5517622758964805 24.666514511715505 chr14 107349540 46839935 0.43633102666299267 11.061025078791518 chr15 102531392 150566214 1.4684889287370642 310.7860500315975 chr16 90354753 25907947 0.28673585107360094 11.109847638042844 chr17 81195210 20544551 0.253026637901423 6.060881332446339 chr18 78077248 29413519 0.3767233061288226 6.646513174411072 chr19 59128983 7311895 0.12366008392195753 7.008806893800209 chr20 63025520 22274116 0.3534142360110635 6.691238034217529 chr21 48129895 6322061 0.13135414070610377 5.051809291158272 chr22 51304566 7845008 0.1529105226228792 32.35263890359312 chrMT 16571 58906475 3554.7930118882387 3431.853220578105 chrX 155270560 49816089 0.3208340911503121 14.195491164011168 chrY 59373566 8781151 0.1478966414110953 3.195781249901986