BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975299.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 54,716,628 number of mapped reads = 54,527,324 (99.65%) number of supplementary alignments = 126,806 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,286,812 number of mapped paired reads (second in pair) = 27,240,512 number of mapped paired reads (both in pair) = 54,432,548 number of mapped paired reads (singletons) = 94,776 number of mapped bases = 4,942,780,599 bp number of sequenced bases = 4,941,180,303 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,447,220 duplication rate = 45.18% >>>>>>> Insert size mean insert size = 97,939.486 std insert size = 3,076,286.9933 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 55.7581 >>>>>>> ACTG content number of A's = 1,332,726,815 bp (26.97%) number of C's = 1,037,844,832 bp (21%) number of T's = 1,390,484,079 bp (28.14%) number of G's = 1,179,913,303 bp (23.88%) number of N's = 211,274 bp (0%) GC percentage = 44.88% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 26,117,784 number of insertions = 454,734 mapped reads with insertion percentage = 0.82% number of deletions = 1,000,403 mapped reads with deletion percentage = 1.81% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 1.5967X std coverageData = 25.7736X There is a 11.95% of reference with a coverageData >= 1X There is a 6.34% of reference with a coverageData >= 2X There is a 3.78% of reference with a coverageData >= 3X There is a 2.75% of reference with a coverageData >= 4X There is a 2.13% of reference with a coverageData >= 5X There is a 1.81% of reference with a coverageData >= 6X There is a 1.6% of reference with a coverageData >= 7X There is a 1.46% of reference with a coverageData >= 8X There is a 1.35% of reference with a coverageData >= 9X There is a 1.28% of reference with a coverageData >= 10X There is a 1.21% of reference with a coverageData >= 11X There is a 1.16% of reference with a coverageData >= 12X There is a 1.12% of reference with a coverageData >= 13X There is a 1.08% of reference with a coverageData >= 14X There is a 1.05% of reference with a coverageData >= 15X There is a 1.02% of reference with a coverageData >= 16X There is a 0.99% of reference with a coverageData >= 17X There is a 0.96% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.92% of reference with a coverageData >= 20X There is a 0.9% of reference with a coverageData >= 21X There is a 0.88% of reference with a coverageData >= 22X There is a 0.86% of reference with a coverageData >= 23X There is a 0.84% of reference with a coverageData >= 24X There is a 0.83% of reference with a coverageData >= 25X There is a 0.81% of reference with a coverageData >= 26X There is a 0.8% of reference with a coverageData >= 27X There is a 0.78% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.76% of reference with a coverageData >= 30X There is a 0.74% of reference with a coverageData >= 31X There is a 0.73% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.71% of reference with a coverageData >= 34X There is a 0.7% of reference with a coverageData >= 35X There is a 0.69% of reference with a coverageData >= 36X There is a 0.68% of reference with a coverageData >= 37X There is a 0.67% of reference with a coverageData >= 38X There is a 0.66% of reference with a coverageData >= 39X There is a 0.65% of reference with a coverageData >= 40X There is a 0.64% of reference with a coverageData >= 41X There is a 0.63% of reference with a coverageData >= 42X There is a 0.62% of reference with a coverageData >= 43X There is a 0.61% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.6% of reference with a coverageData >= 46X There is a 0.59% of reference with a coverageData >= 47X There is a 0.58% of reference with a coverageData >= 48X There is a 0.58% of reference with a coverageData >= 49X There is a 0.57% of reference with a coverageData >= 50X There is a 0.56% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 563984897 2.2627221337996186 31.479148095623497 chr2 243199373 384051454 1.579163010424373 24.56100176631 chr3 198022430 228583303 1.1543303604546211 19.853964395149035 chr4 191154276 248859381 1.3018771340485211 22.741429925677505 chr5 180915260 261217430 1.4438662056478817 23.28470955231412 chr6 171115067 440862340 2.5764086572224527 41.09816278975474 chr7 159138663 256089166 1.6092202936253146 26.584933618359678 chr8 146364022 197798902 1.351417508873868 22.451916731280676 chr9 141213431 172766990 1.2234458774675618 20.721655775924088 chr10 135534747 227494850 1.6784983558496627 26.07687538339242 chr11 135006516 206471374 1.5293437688592748 23.25808206471656 chr12 133851895 275007442 2.0545651744414974 27.728115890218195 chr13 115169878 97358954 0.8453508477277366 17.107697573641328 chr14 107349540 174084136 1.6216570280599245 26.336612996105178 chr15 102531392 176033340 1.716872623752148 27.543213042131747 chr16 90354753 146068781 1.6166142471774563 23.844311757379 chr17 81195210 176465057 2.1733431935208984 27.15345415494255 chr18 78077248 108559918 1.3904168087481772 27.706995443518885 chr19 59128983 190599908 3.2234599401109265 33.19819258928847 chr20 63025520 116651487 1.850861159098727 27.68753018447397 chr21 48129895 52141704 1.083353786664193 20.68954276420881 chr22 51304566 80574308 1.5705094942231848 25.074215258329776 chrMT 16571 226955 13.695914549514212 23.065999538628446 chrX 155270560 143805365 0.926159891482326 19.09588918293959 chrY 59373566 17023157 0.28671272667031655 6.810592088545317