BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961007.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 387,313,726 number of mapped reads = 379,602,631 (98.01%) number of supplementary alignments = 814,439 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,049,956 number of mapped paired reads (second in pair) = 189,552,675 number of mapped paired reads (both in pair) = 378,530,632 number of mapped paired reads (singletons) = 1,071,999 number of mapped bases = 37,060,070,222 bp number of sequenced bases = 37,048,663,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,388,113 duplication rate = 12.02% >>>>>>> Insert size mean insert size = 15,835.5316 std insert size = 1,210,830.0605 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 53.5867 >>>>>>> ACTG content number of A's = 10,980,845,272 bp (29.64%) number of C's = 7,523,542,181 bp (20.31%) number of T's = 10,926,214,926 bp (29.49%) number of G's = 7,600,541,736 bp (20.52%) number of N's = 17,519,586 bp (0.05%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 204,762,112 number of insertions = 3,804,882 mapped reads with insertion percentage = 0.97% number of deletions = 4,472,659 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.14% >>>>>>> Coverage mean coverageData = 11.9715X std coverageData = 141.5356X There is a 91.21% of reference with a coverageData >= 1X There is a 90.52% of reference with a coverageData >= 2X There is a 88.93% of reference with a coverageData >= 3X There is a 86.78% of reference with a coverageData >= 4X There is a 83.5% of reference with a coverageData >= 5X There is a 79.56% of reference with a coverageData >= 6X There is a 74.66% of reference with a coverageData >= 7X There is a 69.32% of reference with a coverageData >= 8X There is a 63.47% of reference with a coverageData >= 9X There is a 57.53% of reference with a coverageData >= 10X There is a 51.51% of reference with a coverageData >= 11X There is a 45.69% of reference with a coverageData >= 12X There is a 40.1% of reference with a coverageData >= 13X There is a 34.88% of reference with a coverageData >= 14X There is a 30.05% of reference with a coverageData >= 15X There is a 25.68% of reference with a coverageData >= 16X There is a 21.76% of reference with a coverageData >= 17X There is a 18.3% of reference with a coverageData >= 18X There is a 15.27% of reference with a coverageData >= 19X There is a 12.66% of reference with a coverageData >= 20X There is a 10.44% of reference with a coverageData >= 21X There is a 8.56% of reference with a coverageData >= 22X There is a 6.98% of reference with a coverageData >= 23X There is a 5.68% of reference with a coverageData >= 24X There is a 4.6% of reference with a coverageData >= 25X There is a 3.73% of reference with a coverageData >= 26X There is a 3.01% of reference with a coverageData >= 27X There is a 2.44% of reference with a coverageData >= 28X There is a 1.97% of reference with a coverageData >= 29X There is a 1.6% of reference with a coverageData >= 30X There is a 1.31% of reference with a coverageData >= 31X There is a 1.07% of reference with a coverageData >= 32X There is a 0.88% of reference with a coverageData >= 33X There is a 0.73% of reference with a coverageData >= 34X There is a 0.62% of reference with a coverageData >= 35X There is a 0.52% of reference with a coverageData >= 36X There is a 0.45% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.34% of reference with a coverageData >= 39X There is a 0.31% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3197494830 12.828432752430334 340.1459141157459 chr2 243199373 3828177901 15.740903661786989 82.85432600395066 chr3 198022430 2369642204 11.966534316339821 42.072462403532924 chr4 191154276 1975080126 10.332387887572025 116.60661777420061 chr5 180915260 1946587588 10.759664983484534 13.066884088321082 chr6 171115067 2200970310 12.8625161336611 41.34527887728963 chr7 159138663 1906652480 11.981076402533304 87.16215955777406 chr8 146364022 2077395710 14.193349442119047 133.08128733312424 chr9 141213431 1872208828 13.25800821311395 94.72580502797084 chr10 135534747 1635688184 12.0684047464227 348.93598582832163 chr11 135006516 1654856657 12.257605825484749 54.24337826623588 chr12 133851895 1864274190 13.927887909244767 12.783697947673396 chr13 115169878 1005647996 8.731866469460009 7.610795356391378 chr14 107349540 738645629 6.880752623625588 12.164611601614155 chr15 102531392 937387495 9.142443857584611 7.327548081281119 chr16 90354753 1070227684 11.844730337539632 133.22384589722463 chr17 81195210 898837770 11.07008369089753 36.619939562017926 chr18 78077248 1133871523 14.522431976598355 125.55029568931442 chr19 59128983 771759876 13.05214189122786 171.52129375850168 chr20 63025520 784720931 12.450844213582053 37.336211623716196 chr21 48129895 456409752 9.482874458795308 64.07452629584247 chr22 51304566 514094118 10.02043595885793 11.326449415893912 chrMT 16571 17432739 1052.0028362802486 178.4499569132664 chrX 155270560 2081167870 13.403493038216645 42.34973578536472 chrY 59373566 120837831 2.035212623072025 124.85710302444592