BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038451.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 = 15,114,194 number of mapped reads = 14,398,463 (95.26%) number of supplementary alignments = 316,699 (2.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,262,172 number of mapped paired reads (second in pair) = 7,136,291 number of mapped paired reads (both in pair) = 14,242,234 number of mapped paired reads (singletons) = 156,229 number of mapped bases = 2,062,374,351 bp number of sequenced bases = 2,060,657,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,929,399 duplication rate = 10.6% >>>>>>> Insert size mean insert size = 72,020.4948 std insert size = 2,456,077.251 median insert size = 246 >>>>>>> Mapping quality mean mapping quality = 53.5616 >>>>>>> ACTG content number of A's = 613,881,952 bp (29.79%) number of C's = 412,730,301 bp (20.03%) number of T's = 612,311,264 bp (29.71%) number of G's = 421,688,954 bp (20.46%) number of N's = 44,682 bp (0%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0159 number of mismatches = 31,320,534 number of insertions = 450,253 mapped reads with insertion percentage = 2.9% number of deletions = 775,206 mapped reads with deletion percentage = 5.15% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.6662X std coverageData = 15.2855X There is a 26.17% of reference with a coverageData >= 1X There is a 14.35% of reference with a coverageData >= 2X There is a 7.39% of reference with a coverageData >= 3X There is a 4.34% of reference with a coverageData >= 4X There is a 2.46% of reference with a coverageData >= 5X There is a 1.48% of reference with a coverageData >= 6X There is a 0.89% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% 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 0.04% 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 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% 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 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 120360449 0.48288926429595536 21.825136901649298 chr2 243199373 212416016 0.873423370215679 19.562009269262944 chr3 198022430 129649671 0.6547221494049942 1.5729314928367009 chr4 191154276 136540643 0.7142955201274179 17.618025675152882 chr5 180915260 132654651 0.7332419111577432 1.813257899868329 chr6 171115067 145508874 0.8503568771065613 19.070651060559502 chr7 159138663 140535780 0.883102681338978 13.554062847250858 chr8 146364022 98605601 0.6737010889192427 3.8725246331175716 chr9 141213431 81860969 0.5796967641130396 23.048629161456386 chr10 135534747 95505087 0.7046538921860385 31.77945417719481 chr11 135006516 85716777 0.6349084439746597 7.268807056633867 chr12 133851895 67331921 0.5030330052480766 1.347654322146125 chr13 115169878 130611144 1.1340738244074549 2.0633360960859806 chr14 107349540 35759550 0.33311321129089144 1.3983150915586176 chr15 102531392 41171876 0.40155385776875047 1.0839734625424722 chr16 90354753 76117523 0.8424296506017785 20.500620788712407 chr17 81195210 39643365 0.4882475825852289 6.673695723420365 chr18 78077248 35270865 0.4517431890017435 19.266409147102355 chr19 59128983 22650328 0.38306642277273734 12.23296699516922 chr20 63025520 51642063 0.8193833704188399 5.278710790407336 chr21 48129895 18845482 0.39155460447191914 8.043224753503264 chr22 51304566 9191596 0.1791574652439317 0.8435870036815089 chrMT 16571 4308035 259.9743527849858 153.08844808137744 chrX 155270560 99272527 0.6393518964573838 2.3726490076714337 chrY 59373566 51203558 0.8623965419223767 29.167575876112394