BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238496.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,023,154 number of mapped reads = 3,061,348 (76.09%) number of supplementary alignments = 25,349 (0.63%) number of secondary alignments = 0 number of mapped bases = 187,587,991 bp number of sequenced bases = 187,515,274 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,238,853 duplication rate = 22.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1796 >>>>>>> ACTG content number of A's = 46,425,693 bp (24.76%) number of C's = 33,073,216 bp (17.64%) number of T's = 62,726,019 bp (33.45%) number of G's = 45,286,095 bp (24.15%) number of N's = 4,251 bp (0%) GC percentage = 41.79% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,053,667 number of insertions = 12,399 mapped reads with insertion percentage = 0.4% number of deletions = 42,241 mapped reads with deletion percentage = 1.37% homopolymer indels = 42.74% >>>>>>> Coverage mean coverageData = 0.0606X std coverageData = 1.1387X There is a 1.67% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 13183300 0.05289174384845364 1.6219372996836614 chr2 243199373 14704631 0.06046327677004332 2.1827726878415166 chr3 198022430 11923752 0.06021414846792861 0.7664791194705365 chr4 191154276 11914473 0.062329094851113875 0.7826533553456955 chr5 180915260 10098512 0.055819017146480625 0.7053963460772543 chr6 171115067 9627530 0.05626348496827576 0.9620699218623809 chr7 159138663 8685797 0.05458005513091435 0.8876837983824755 chr8 146364022 10407553 0.07110731761662029 0.994432880288781 chr9 141213431 12301318 0.08711152978076143 0.9578436242766064 chr10 135534747 7764975 0.05729139701717966 0.8630331039082653 chr11 135006516 9237385 0.06842177158323233 0.811284372617195 chr12 133851895 9957856 0.07439458365531545 0.8656461804694691 chr13 115169878 6362671 0.05524596457417451 0.8694516363399841 chr14 107349540 5563110 0.05182239253191025 1.0511936961613382 chr15 102531392 6351480 0.06194668653284255 1.4730537880094592 chr16 90354753 5153229 0.05703329187342253 0.7490135838727109 chr17 81195210 4406929 0.054275726363661105 0.7184087342890093 chr18 78077248 6070814 0.07775394440131907 1.6106344357769424 chr19 59128983 4056624 0.06860635502558872 1.1423539696792857 chr20 63025520 3562562 0.05652570577759612 0.7288987919310278 chr21 48129895 2932433 0.060927475532618555 0.7557735572077385 chr22 51304566 2374270 0.046277947268864916 0.9124932240654631 chrMT 16571 35554 2.145555488504013 3.6432345615324744 chrX 155270560 10327752 0.06651455369259955 0.8614883303905402 chrY 59373566 583481 0.009827285765520636 0.3690268081592178