BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472774.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 = 17,952,916
number of mapped reads = 17,745,972 (98.85%)
number of supplementary alignments = 61,774 (0.34%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 8,915,428
number of mapped paired reads (second in pair) = 8,830,544
number of mapped paired reads (both in pair) = 17,619,368
number of mapped paired reads (singletons) = 126,604
number of mapped bases = 1,749,623,479 bp
number of sequenced bases = 1,749,379,678 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 11,188,212
duplication rate = 47.18%
>>>>>>> Insert size
mean insert size = 23,391.8397
std insert size = 1,515,997.8217
median insert size = 264
>>>>>>> Mapping quality
mean mapping quality = 55.0992
>>>>>>> ACTG content
number of A's = 485,328,879 bp (27.74%)
number of C's = 392,127,298 bp (22.42%)
number of T's = 482,483,908 bp (27.58%)
number of G's = 389,107,211 bp (22.24%)
number of N's = 332,382 bp (0.02%)
GC percentage = 44.66%
>>>>>>> Mismatches and indels
general error rate = 0.0069
number of mismatches = 11,908,137
number of insertions = 109,477
mapped reads with insertion percentage = 0.61%
number of deletions = 96,784
mapped reads with deletion percentage = 0.54%
homopolymer indels = 46.01%
>>>>>>> Coverage
mean coverageData = 0.5652X
std coverageData = 18.1623X
There is a 4.94% of reference with a coverageData >= 1X
There is a 2.06% of reference with a coverageData >= 2X
There is a 0.95% of reference with a coverageData >= 3X
There is a 0.68% of reference with a coverageData >= 4X
There is a 0.53% of reference with a coverageData >= 5X
There is a 0.47% of reference with a coverageData >= 6X
There is a 0.43% of reference with a coverageData >= 7X
There is a 0.41% of reference with a coverageData >= 8X
There is a 0.39% of reference with a coverageData >= 9X
There is a 0.37% of reference with a coverageData >= 10X
There is a 0.36% of reference with a coverageData >= 11X
There is a 0.35% of reference with a coverageData >= 12X
There is a 0.33% of reference with a coverageData >= 13X
There is a 0.33% of reference with a coverageData >= 14X
There is a 0.32% of reference with a coverageData >= 15X
There is a 0.31% of reference with a coverageData >= 16X
There is a 0.3% of reference with a coverageData >= 17X
There is a 0.29% of reference with a coverageData >= 18X
There is a 0.29% of reference with a coverageData >= 19X
There is a 0.28% of reference with a coverageData >= 20X
There is a 0.27% of reference with a coverageData >= 21X
There is a 0.27% of reference with a coverageData >= 22X
There is a 0.26% of reference with a coverageData >= 23X
There is a 0.26% of reference with a coverageData >= 24X
There is a 0.25% of reference with a coverageData >= 25X
There is a 0.25% of reference with a coverageData >= 26X
There is a 0.24% of reference with a coverageData >= 27X
There is a 0.24% of reference with a coverageData >= 28X
There is a 0.24% of reference with a coverageData >= 29X
There is a 0.23% of reference with a coverageData >= 30X
There is a 0.23% of reference with a coverageData >= 31X
There is a 0.22% of reference with a coverageData >= 32X
There is a 0.22% of reference with a coverageData >= 33X
There is a 0.22% of reference with a coverageData >= 34X
There is a 0.21% of reference with a coverageData >= 35X
There is a 0.21% of reference with a coverageData >= 36X
There is a 0.21% of reference with a coverageData >= 37X
There is a 0.21% of reference with a coverageData >= 38X
There is a 0.2% of reference with a coverageData >= 39X
There is a 0.2% of reference with a coverageData >= 40X
There is a 0.2% of reference with a coverageData >= 41X
There is a 0.19% of reference with a coverageData >= 42X
There is a 0.19% of reference with a coverageData >= 43X
There is a 0.19% of reference with a coverageData >= 44X
There is a 0.19% 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 0.18% of reference with a coverageData >= 48X
There is a 0.18% of reference with a coverageData >= 49X
There is a 0.18% of reference with a coverageData >= 50X
There is a 0.17% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 234347228 0.9402071981196789 29.461639159852762
chr2 243199373 70169859 0.28852812461815025 10.735085957315931
chr3 198022430 203593689 1.0281344845631881 22.503411216585224
chr4 191154276 61737819 0.3229737795664063 13.717732282732607
chr5 180915260 82091563 0.45375698545274734 13.071018816641496
chr6 171115067 112228824 0.6558675747706074 18.686576683661414
chr7 159138663 88138770 0.553848878320663 20.629814648470266
chr8 146364022 71456444 0.4882104428641623 14.661953527523039
chr9 141213431 113335918 0.8025859664864314 19.263846859532656
chr10 135534747 36861593 0.27197153361713217 11.085886793984283
chr11 135006516 77981280 0.5776112317423256 18.75382414793843
chr12 133851895 90732497 0.6778573960420956 18.253046458107374
chr13 115169878 49719397 0.431704868177424 16.86924088255876
chr14 107349540 65741683 0.6124076824176424 25.68597557711463
chr15 102531392 38559891 0.3760788793348285 12.647368133348827
chr16 90354753 76714918 0.8490413116396877 20.167041054169278
chr17 81195210 83495168 1.0283262768825896 24.594700772823593
chr18 78077248 25863728 0.3312581918870911 11.151238923905106
chr19 59128983 31470721 0.5322384963056104 14.683402594848827
chr20 63025520 30684568 0.4868594182166208 18.89428770142785
chr21 48129895 8255475 0.1715248911305541 7.927383877490487
chr22 51304566 18833642 0.36709485077799897 11.15266290960554
chrMT 16571 10714 0.646551203910446 1.6735733897778102
chrX 155270560 70724054 0.4554891410193922 13.22039163463884
chrY 59373566 6874036 0.11577603406876387 5.808851422817759