BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618632.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 151,321,526 number of mapped reads = 145,706,591 (96.29%) number of supplementary alignments = 239,638 (0.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 73,375,396 number of mapped paired reads (second in pair) = 72,331,195 number of mapped paired reads (both in pair) = 142,740,870 number of mapped paired reads (singletons) = 2,965,721 number of mapped bases = 13,832,714,187 bp number of sequenced bases = 13,823,698,548 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,722,771 duplication rate = 33.74% >>>>>>> Insert size mean insert size = 30,402.5379 std insert size = 1,746,117.1317 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 52.3232 >>>>>>> ACTG content number of A's = 3,652,203,200 bp (26.42%) number of C's = 3,184,844,926 bp (23.04%) number of T's = 3,673,707,830 bp (26.58%) number of G's = 3,307,017,348 bp (23.92%) number of N's = 5,925,244 bp (0.04%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 188,268,907 number of insertions = 2,555,219 mapped reads with insertion percentage = 1.72% number of deletions = 6,456,701 mapped reads with deletion percentage = 4.32% homopolymer indels = 51.64% >>>>>>> Coverage mean coverageData = 4.4684X std coverageData = 18.5625X There is a 38.85% of reference with a coverageData >= 1X There is a 30.83% of reference with a coverageData >= 2X There is a 25.8% of reference with a coverageData >= 3X There is a 22.26% of reference with a coverageData >= 4X There is a 19.52% of reference with a coverageData >= 5X There is a 17.34% of reference with a coverageData >= 6X There is a 15.54% of reference with a coverageData >= 7X There is a 14.05% of reference with a coverageData >= 8X There is a 12.78% of reference with a coverageData >= 9X There is a 11.69% of reference with a coverageData >= 10X There is a 10.74% of reference with a coverageData >= 11X There is a 9.91% of reference with a coverageData >= 12X There is a 9.18% of reference with a coverageData >= 13X There is a 8.53% of reference with a coverageData >= 14X There is a 7.94% of reference with a coverageData >= 15X There is a 7.42% of reference with a coverageData >= 16X There is a 6.95% of reference with a coverageData >= 17X There is a 6.53% of reference with a coverageData >= 18X There is a 6.14% of reference with a coverageData >= 19X There is a 5.79% of reference with a coverageData >= 20X There is a 5.46% of reference with a coverageData >= 21X There is a 5.16% of reference with a coverageData >= 22X There is a 4.89% of reference with a coverageData >= 23X There is a 4.64% of reference with a coverageData >= 24X There is a 4.4% of reference with a coverageData >= 25X There is a 4.19% of reference with a coverageData >= 26X There is a 3.98% of reference with a coverageData >= 27X There is a 3.8% of reference with a coverageData >= 28X There is a 3.62% of reference with a coverageData >= 29X There is a 3.46% of reference with a coverageData >= 30X There is a 3.3% of reference with a coverageData >= 31X There is a 3.16% of reference with a coverageData >= 32X There is a 3.03% of reference with a coverageData >= 33X There is a 2.9% of reference with a coverageData >= 34X There is a 2.78% of reference with a coverageData >= 35X There is a 2.67% of reference with a coverageData >= 36X There is a 2.56% of reference with a coverageData >= 37X There is a 2.46% of reference with a coverageData >= 38X There is a 2.37% of reference with a coverageData >= 39X There is a 2.28% of reference with a coverageData >= 40X There is a 2.19% of reference with a coverageData >= 41X There is a 2.11% of reference with a coverageData >= 42X There is a 2.03% of reference with a coverageData >= 43X There is a 1.96% of reference with a coverageData >= 44X There is a 1.89% of reference with a coverageData >= 45X There is a 1.83% of reference with a coverageData >= 46X There is a 1.76% of reference with a coverageData >= 47X There is a 1.7% of reference with a coverageData >= 48X There is a 1.65% of reference with a coverageData >= 49X There is a 1.59% of reference with a coverageData >= 50X There is a 1.54% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1224865137 4.914190913891444 19.25307513488899 chr2 243199373 1055929371 4.341826041632106 22.693629271349216 chr3 198022430 861559079 4.35081560710067 13.495037553522515 chr4 191154276 589060752 3.0815986140953497 14.566361288620996 chr5 180915260 827900249 4.576176984738601 14.382253764695225 chr6 171115067 770052828 4.500204695592353 14.693807278013235 chr7 159138663 706870683 4.441853850437338 13.520549393652997 chr8 146364022 745327576 5.092286791626975 16.213104444593565 chr9 141213431 614731151 4.353205970896635 16.870366198413787 chr10 135534747 744640956 5.494096329408428 16.331214754717212 chr11 135006516 643837766 4.768938456274214 15.990108593165358 chr12 133851895 617364719 4.612297188620303 14.73142591864569 chr13 115169878 355977013 3.0908864295228304 11.36060202963043 chr14 107349540 506077087 4.7142920873252 16.247902369322123 chr15 102531392 482904584 4.709821788043217 15.480812912555367 chr16 90354753 574625993 6.359665362595812 46.92057966713635 chr17 81195210 544447489 6.705413890794789 20.136206908972387 chr18 78077248 388710211 4.978533708052825 17.941604252350743 chr19 59128983 357996069 6.054493935740448 19.77269115793932 chr20 63025520 504639890 8.006913548670443 22.496966197103298 chr21 48129895 179957591 3.7389982047540307 31.276695803479093 chr22 51304566 397321878 7.744376553151234 25.490271796257503 chrMT 16571 9354 0.5644801158650655 3.1923243700504123 chrX 155270560 20591973 0.13261994418001713 3.018850727093361 chrY 59373566 117314788 1.9758757289397104 19.49150669295598