BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472543.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 = 20,467,332
number of mapped reads = 20,244,850 (98.91%)
number of supplementary alignments = 81,280 (0.4%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 10,146,181
number of mapped paired reads (second in pair) = 10,098,669
number of mapped paired reads (both in pair) = 20,139,176
number of mapped paired reads (singletons) = 105,674
number of mapped bases = 1,992,973,628 bp
number of sequenced bases = 1,992,711,845 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 13,339,862
duplication rate = 46.82%
>>>>>>> Insert size
mean insert size = 28,044.8956
std insert size = 1,643,657.3915
median insert size = 231
>>>>>>> Mapping quality
mean mapping quality = 55.0796
>>>>>>> ACTG content
number of A's = 539,920,810 bp (27.09%)
number of C's = 459,403,203 bp (23.05%)
number of T's = 536,286,689 bp (26.91%)
number of G's = 456,792,335 bp (22.92%)
number of N's = 308,808 bp (0.02%)
GC percentage = 45.98%
>>>>>>> Mismatches and indels
general error rate = 0.006
number of mismatches = 11,653,905
number of insertions = 105,581
mapped reads with insertion percentage = 0.52%
number of deletions = 98,428
mapped reads with deletion percentage = 0.48%
homopolymer indels = 44.95%
>>>>>>> Coverage
mean coverageData = 0.6438X
std coverageData = 23.8952X
There is a 6.03% of reference with a coverageData >= 1X
There is a 2.72% of reference with a coverageData >= 2X
There is a 1.16% of reference with a coverageData >= 3X
There is a 0.79% of reference with a coverageData >= 4X
There is a 0.54% of reference with a coverageData >= 5X
There is a 0.46% of reference with a coverageData >= 6X
There is a 0.41% of reference with a coverageData >= 7X
There is a 0.38% of reference with a coverageData >= 8X
There is a 0.36% of reference with a coverageData >= 9X
There is a 0.34% of reference with a coverageData >= 10X
There is a 0.33% of reference with a coverageData >= 11X
There is a 0.32% of reference with a coverageData >= 12X
There is a 0.31% of reference with a coverageData >= 13X
There is a 0.3% of reference with a coverageData >= 14X
There is a 0.29% of reference with a coverageData >= 15X
There is a 0.28% of reference with a coverageData >= 16X
There is a 0.28% of reference with a coverageData >= 17X
There is a 0.27% of reference with a coverageData >= 18X
There is a 0.26% of reference with a coverageData >= 19X
There is a 0.26% of reference with a coverageData >= 20X
There is a 0.25% of reference with a coverageData >= 21X
There is a 0.25% of reference with a coverageData >= 22X
There is a 0.24% of reference with a coverageData >= 23X
There is a 0.24% of reference with a coverageData >= 24X
There is a 0.24% of reference with a coverageData >= 25X
There is a 0.23% of reference with a coverageData >= 26X
There is a 0.23% of reference with a coverageData >= 27X
There is a 0.22% of reference with a coverageData >= 28X
There is a 0.22% of reference with a coverageData >= 29X
There is a 0.22% of reference with a coverageData >= 30X
There is a 0.21% of reference with a coverageData >= 31X
There is a 0.21% of reference with a coverageData >= 32X
There is a 0.21% of reference with a coverageData >= 33X
There is a 0.21% of reference with a coverageData >= 34X
There is a 0.2% of reference with a coverageData >= 35X
There is a 0.2% of reference with a coverageData >= 36X
There is a 0.2% of reference with a coverageData >= 37X
There is a 0.19% of reference with a coverageData >= 38X
There is a 0.19% of reference with a coverageData >= 39X
There is a 0.19% of reference with a coverageData >= 40X
There is a 0.19% of reference with a coverageData >= 41X
There is a 0.19% of reference with a coverageData >= 42X
There is a 0.18% of reference with a coverageData >= 43X
There is a 0.18% of reference with a coverageData >= 44X
There is a 0.18% of reference with a coverageData >= 45X
There is a 0.18% 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 0.17% of reference with a coverageData >= 49X
There is a 0.17% of reference with a coverageData >= 50X
There is a 0.17% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 243162095 0.9755726747015808 33.71468784060879
chr2 243199373 138030020 0.5675591112646495 17.641157206885907
chr3 198022430 235172330 1.1876045052068092 30.822651258018528
chr4 191154276 57260617 0.29955184994135314 10.56617345055908
chr5 180915260 90393972 0.499648133606861 16.247854885680137
chr6 171115067 114104041 0.6668263818054082 22.673061947226735
chr7 159138663 82067887 0.5157004932233219 17.11717487398173
chr8 146364022 72202313 0.49330642881622916 17.49864652648564
chr9 141213431 131081326 0.9282497073525534 29.115943533006917
chr10 135534747 50354915 0.37152771606236146 15.344331507114978
chr11 135006516 91662165 0.6789462295286548 32.81653765070926
chr12 133851895 96611227 0.721777058143256 22.984095015484844
chr13 115169878 54664935 0.47464611363051024 22.097002466761946
chr14 107349540 68592420 0.638963334169853 22.763077153037965
chr15 102531392 59762966 0.5828748135985513 32.488771748567075
chr16 90354753 61796537 0.6839323328126413 18.26216469217834
chr17 81195210 106916750 1.316786421267954 53.96466450233015
chr18 78077248 34225980 0.43836048114810605 14.822572524978852
chr19 59128983 48488478 0.8200458648172589 22.580877499615596
chr20 63025520 27428817 0.4352017563678967 11.527680345450012
chr21 48129895 9899044 0.20567350084599187 7.259875373297301
chr22 51304566 20037968 0.39056890180105996 11.123116391028475
chrMT 16571 4117 0.24844608050208195 0.6136285540434481
chrX 155270560 94008570 0.6054500608486245 18.00447003498699
chrY 59373566 5044138 0.08495595497834844 6.380310564754175