BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777285.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 = 256,472,912 number of mapped reads = 253,258,871 (98.75%) number of supplementary alignments = 935,289 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 126,893,487 number of mapped paired reads (second in pair) = 126,365,384 number of mapped paired reads (both in pair) = 252,183,910 number of mapped paired reads (singletons) = 1,074,961 number of mapped bases = 24,486,229,162 bp number of sequenced bases = 24,479,288,382 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,252,126 duplication rate = 8.49% >>>>>>> Insert size mean insert size = 106,069.2618 std insert size = 3,183,193.6962 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 53.5642 >>>>>>> ACTG content number of A's = 7,098,408,466 bp (29%) number of C's = 5,116,235,680 bp (20.9%) number of T's = 6,984,486,438 bp (28.53%) number of G's = 5,250,727,726 bp (21.45%) number of N's = 29,430,072 bp (0.12%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 219,646,732 number of insertions = 2,444,728 mapped reads with insertion percentage = 0.94% number of deletions = 2,933,822 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 7.9098X std coverageData = 97.478X There is a 91.68% of reference with a coverageData >= 1X There is a 90.04% of reference with a coverageData >= 2X There is a 86.94% of reference with a coverageData >= 3X There is a 82.13% of reference with a coverageData >= 4X There is a 75.55% of reference with a coverageData >= 5X There is a 67.43% of reference with a coverageData >= 6X There is a 58.25% of reference with a coverageData >= 7X There is a 48.63% of reference with a coverageData >= 8X There is a 39.23% of reference with a coverageData >= 9X There is a 30.59% of reference with a coverageData >= 10X There is a 23.08% of reference with a coverageData >= 11X There is a 16.89% of reference with a coverageData >= 12X There is a 12.01% of reference with a coverageData >= 13X There is a 8.33% of reference with a coverageData >= 14X There is a 5.66% of reference with a coverageData >= 15X There is a 3.8% of reference with a coverageData >= 16X There is a 2.53% of reference with a coverageData >= 17X There is a 1.69% of reference with a coverageData >= 18X There is a 1.15% of reference with a coverageData >= 19X There is a 0.81% of reference with a coverageData >= 20X There is a 0.59% of reference with a coverageData >= 21X There is a 0.46% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.32% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2052971691 8.236576032442462 231.22868628296058 chr2 243199373 2098642638 8.62930941026727 58.67507235674922 chr3 198022430 1604436252 8.1022955429847 21.374609120621802 chr4 191154276 1585366680 8.293650098625049 61.945265175949565 chr5 180915260 1459965088 8.069883590803784 8.612176957208863 chr6 171115067 1407331240 8.22447295070749 50.3588495977067 chr7 159138663 1326472096 8.335322611074092 80.09927491755593 chr8 146364022 1214063935 8.294824905809161 29.744807657170934 chr9 141213431 1055129505 7.471877834339993 86.6878731366305 chr10 135534747 1359965076 10.0340695364267 255.23448125363825 chr11 135006516 1153612723 8.544866997382556 52.750865608704395 chr12 133851895 1094698305 8.178429636726474 7.8108628860789535 chr13 115169878 755230062 6.557531145426759 4.9072257168020235 chr14 107349540 743860827 6.929334089368245 8.876864921744335 chr15 102531392 709599070 6.920798168818385 5.313686466647079 chr16 90354753 780779472 8.641266187734473 39.64743749723097 chr17 81195210 732615149 9.02288631312118 52.005830711798744 chr18 78077248 676503571 8.66454169849839 111.61433242518956 chr19 59128983 541126492 9.151628601493112 107.96877569473229 chr20 63025520 540024883 8.568352676820437 17.02619446366523 chr21 48129895 343682709 7.140732573798467 29.61209380244476 chr22 51304566 324347261 6.321995999342437 12.37493588431646 chrMT 16571 27378970 1652.2219540160522 175.99423340755104 chrX 155270560 658309291 4.239756016852132 23.767754545297983 chrY 59373566 240116176 4.044159584418426 72.39051655926993