BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472679.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,979,008 number of mapped reads = 19,801,820 (99.11%) number of supplementary alignments = 118,721 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,934,108 number of mapped paired reads (second in pair) = 9,867,712 number of mapped paired reads (both in pair) = 19,683,702 number of mapped paired reads (singletons) = 118,118 number of mapped bases = 1,950,280,409 bp number of sequenced bases = 1,949,996,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,076,209 duplication rate = 49.29% >>>>>>> Insert size mean insert size = 21,897.5391 std insert size = 1,472,044.8162 median insert size = 225 >>>>>>> Mapping quality mean mapping quality = 54.5925 >>>>>>> ACTG content number of A's = 523,126,694 bp (26.83%) number of C's = 454,778,197 bp (23.32%) number of T's = 523,256,721 bp (26.83%) number of G's = 448,463,738 bp (23%) number of N's = 371,187 bp (0.02%) GC percentage = 46.32% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 12,454,431 number of insertions = 125,709 mapped reads with insertion percentage = 0.63% number of deletions = 109,052 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.63X std coverageData = 30.5441X There is a 3.86% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% 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 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 215791888 0.8657626895140214 36.12539959308239 chr2 243199373 162884722 0.6697579849434891 33.63651322712534 chr3 198022430 191296273 0.9660333579382901 27.211003417765056 chr4 191154276 56261605 0.29432564197517613 19.629763959432847 chr5 180915260 61165171 0.33808740622543393 21.385956879045807 chr6 171115067 128426271 0.7505257909287438 27.24603558951066 chr7 159138663 118533951 0.74484697034309 32.24853337800939 chr8 146364022 107061738 0.7314757857637992 23.801605396954958 chr9 141213431 117354685 0.8310447821354896 25.962940763937862 chr10 135534747 51870658 0.3827111434383686 16.973426532279962 chr11 135006516 38837832 0.28767375939099116 15.375432681935509 chr12 133851895 78077473 0.5833124215387462 22.971849097019952 chr13 115169878 57517325 0.49941291940936156 19.12346440717776 chr14 107349540 15633412 0.14563091746830029 7.241390828737242 chr15 102531392 20722521 0.20210903798126528 20.03788390197447 chr16 90354753 125642636 1.3905481651861746 55.23417872047002 chr17 81195210 64329477 0.7922816752367535 18.925828924295747 chr18 78077248 12507785 0.16019756485269562 9.182561560762872 chr19 59128983 47643491 0.805755292628659 26.500069340671065 chr20 63025520 77973606 1.2371751315974862 34.061601209438884 chr21 48129895 12018140 0.24970218613608028 14.537697591134412 chr22 51304566 18685257 0.36420261307736235 15.84656787365588 chrMT 16571 2879 0.17373725182547825 0.46924677117142694 chrX 155270560 168226432 1.0834406213257683 73.28807071572564 chrY 59373566 1815181 0.030572207840775474 1.7130676016582322