BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5038458.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 77,682,592
number of mapped reads = 77,426,964 (99.67%)
number of supplementary alignments = 118,884 (0.15%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 38,788,135
number of mapped paired reads (second in pair) = 38,638,829
number of mapped paired reads (both in pair) = 77,252,768
number of mapped paired reads (singletons) = 174,196
number of mapped bases = 11,543,385,283 bp
number of sequenced bases = 11,541,644,492 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 31,112,818
duplication rate = 37.99%
>>>>>>> Insert size
mean insert size = 17,421.779
std insert size = 1,428,244.0607
median insert size = 230
>>>>>>> Mapping quality
mean mapping quality = 55.8346
>>>>>>> ACTG content
number of A's = 2,893,702,646 bp (25.07%)
number of C's = 2,876,545,771 bp (24.92%)
number of T's = 2,921,946,701 bp (25.32%)
number of G's = 2,848,384,983 bp (24.68%)
number of N's = 1,064,391 bp (0.01%)
GC percentage = 49.6%
>>>>>>> Mismatches and indels
general error rate = 0.0041
number of mismatches = 45,863,089
number of insertions = 537,866
mapped reads with insertion percentage = 0.66%
number of deletions = 634,016
mapped reads with deletion percentage = 0.8%
homopolymer indels = 46.73%
>>>>>>> Coverage
mean coverageData = 3.7289X
std coverageData = 23.2788X
There is a 25.17% of reference with a coverageData >= 1X
There is a 15.37% of reference with a coverageData >= 2X
There is a 8.88% of reference with a coverageData >= 3X
There is a 6.83% of reference with a coverageData >= 4X
There is a 5.32% of reference with a coverageData >= 5X
There is a 4.69% of reference with a coverageData >= 6X
There is a 4.24% of reference with a coverageData >= 7X
There is a 3.99% of reference with a coverageData >= 8X
There is a 3.8% of reference with a coverageData >= 9X
There is a 3.67% of reference with a coverageData >= 10X
There is a 3.56% of reference with a coverageData >= 11X
There is a 3.48% of reference with a coverageData >= 12X
There is a 3.4% of reference with a coverageData >= 13X
There is a 3.33% of reference with a coverageData >= 14X
There is a 3.27% of reference with a coverageData >= 15X
There is a 3.21% of reference with a coverageData >= 16X
There is a 3.16% of reference with a coverageData >= 17X
There is a 3.11% of reference with a coverageData >= 18X
There is a 3.06% of reference with a coverageData >= 19X
There is a 3.01% of reference with a coverageData >= 20X
There is a 2.97% of reference with a coverageData >= 21X
There is a 2.93% of reference with a coverageData >= 22X
There is a 2.89% of reference with a coverageData >= 23X
There is a 2.85% of reference with a coverageData >= 24X
There is a 2.82% of reference with a coverageData >= 25X
There is a 2.78% of reference with a coverageData >= 26X
There is a 2.75% of reference with a coverageData >= 27X
There is a 2.71% of reference with a coverageData >= 28X
There is a 2.68% of reference with a coverageData >= 29X
There is a 2.65% of reference with a coverageData >= 30X
There is a 2.62% of reference with a coverageData >= 31X
There is a 2.59% of reference with a coverageData >= 32X
There is a 2.56% of reference with a coverageData >= 33X
There is a 2.53% of reference with a coverageData >= 34X
There is a 2.5% of reference with a coverageData >= 35X
There is a 2.47% of reference with a coverageData >= 36X
There is a 2.44% of reference with a coverageData >= 37X
There is a 2.42% of reference with a coverageData >= 38X
There is a 2.39% of reference with a coverageData >= 39X
There is a 2.36% of reference with a coverageData >= 40X
There is a 2.34% of reference with a coverageData >= 41X
There is a 2.31% of reference with a coverageData >= 42X
There is a 2.29% of reference with a coverageData >= 43X
There is a 2.26% of reference with a coverageData >= 44X
There is a 2.24% of reference with a coverageData >= 45X
There is a 2.22% of reference with a coverageData >= 46X
There is a 2.19% of reference with a coverageData >= 47X
There is a 2.17% of reference with a coverageData >= 48X
There is a 2.15% of reference with a coverageData >= 49X
There is a 2.12% of reference with a coverageData >= 50X
There is a 2.1% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 1174337623 4.711473208325527 26.65083604848708
chr2 243199373 873554480 3.591927352542969 24.323923623455084
chr3 198022430 667136839 3.3689963253152686 21.521283694497782
chr4 191154276 403921751 2.113066782769746 15.629236820689474
chr5 180915260 580282059 3.207479894178081 22.056843585173223
chr6 171115067 583359446 3.409164699681297 21.565619780923857
chr7 159138663 546114208 3.4316877979551705 20.977130429386047
chr8 146364022 462484436 3.1598232248632794 21.967650018463765
chr9 141213431 480974751 3.406012782169424 21.944185243055372
chr10 135534747 453718903 3.3476205404360257 20.621135243835106
chr11 135006516 680687074 5.041883119182188 27.529350820642332
chr12 133851895 607296424 4.53707752139034 25.20633822293277
chr13 115169878 227336527 1.9739234854446923 16.05021834415821
chr14 107349540 398727146 3.7142883518643863 23.051499643335315
chr15 102531392 412131435 4.019563442579615 23.23024683438734
chr16 90354753 495129837 5.479842737216049 29.03005938217556
chr17 81195210 629173711 7.748901825612619 33.034298163146026
chr18 78077248 231953561 2.970821422906709 24.771739253719606
chr19 59128983 621678296 10.51393520500767 37.716946209089336
chr20 63025520 328540276 5.212813412725512 29.44339505407449
chr21 48129895 126018004 2.618289609815272 27.039008946183465
chr22 51304566 197015145 3.840109377399275 20.016771932803888
chrMT 16571 710629 42.883893548971095 14.75872954950428
chrX 155270560 356254149 2.294408862826282 16.07407506951982
chrY 59373566 4848573 0.08166214911194655 2.405730075521764