BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038423.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 15,047,880 number of mapped reads = 14,319,488 (95.16%) number of supplementary alignments = 250,607 (1.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,238,319 number of mapped paired reads (second in pair) = 7,081,169 number of mapped paired reads (both in pair) = 14,140,600 number of mapped paired reads (singletons) = 178,888 number of mapped bases = 2,062,020,294 bp number of sequenced bases = 2,060,485,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,192,116 duplication rate = 9.79% >>>>>>> Insert size mean insert size = 73,647.5127 std insert size = 2,591,726.9936 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 53.6893 >>>>>>> ACTG content number of A's = 598,206,377 bp (29.03%) number of C's = 428,883,358 bp (20.81%) number of T's = 594,703,329 bp (28.86%) number of G's = 438,645,826 bp (21.29%) number of N's = 46,157 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0149 number of mismatches = 29,688,573 number of insertions = 394,732 mapped reads with insertion percentage = 2.58% number of deletions = 739,769 mapped reads with deletion percentage = 4.94% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.6661X std coverageData = 9.7902X There is a 26.37% of reference with a coverageData >= 1X There is a 14.9% of reference with a coverageData >= 2X There is a 8% of reference with a coverageData >= 3X There is a 4.83% of reference with a coverageData >= 4X There is a 2.84% of reference with a coverageData >= 5X There is a 1.76% of reference with a coverageData >= 6X There is a 1.09% of reference with a coverageData >= 7X There is a 0.7% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 163995826 0.6579555362471895 16.25655517731249 chr2 243199373 186789907 0.768052584576359 10.961409640499113 chr3 198022430 134594764 0.6796945376339438 1.52167856453633 chr4 191154276 134461016 0.7034162081731302 8.303574104289728 chr5 180915260 124649773 0.6889953506409575 1.6478782754105386 chr6 171115067 123915962 0.724167451601442 13.32450740174148 chr7 159138663 108744685 0.6833329057188321 8.484100074563052 chr8 146364022 105217303 0.7188740891528658 2.8610644738586144 chr9 141213431 90804100 0.6430273618944928 18.409986377642852 chr10 135534747 108236960 0.7985919654979693 13.996106712098607 chr11 135006516 98745354 0.7314117638588644 8.48286052747063 chr12 133851895 88546648 0.6615270407639727 1.551609824601723 chr13 115169878 62008228 0.5384066483078154 1.33328426215352 chr14 107349540 61218680 0.570274264798899 1.5473554146391575 chr15 102531392 57981378 0.5654987888977456 1.388224413310023 chr16 90354753 68462612 0.7577090272163104 8.533896901913753 chr17 81195210 54695683 0.6736318928173226 12.135633774890964 chr18 78077248 61017015 0.7814954620326782 16.037260564911705 chr19 59128983 34103628 0.5767666932475398 8.471681151899078 chr20 63025520 44493250 0.7059560952452276 2.8191221686659436 chr21 48129895 27627079 0.5740107889285858 3.7357692344590325 chr22 51304566 21940551 0.427652989014662 1.3146807799259235 chrMT 16571 9032061 545.0522599722407 383.49608680545185 chrX 155270560 63628196 0.40978918347431736 2.3745947361718693 chrY 59373566 27109635 0.45659435379037194 10.842568957083126