BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472426.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 = 17,440,822
number of mapped reads = 17,232,196 (98.8%)
number of supplementary alignments = 66,915 (0.38%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 8,643,182
number of mapped paired reads (second in pair) = 8,589,014
number of mapped paired reads (both in pair) = 17,130,896
number of mapped paired reads (singletons) = 101,300
number of mapped bases = 1,687,021,538 bp
number of sequenced bases = 1,686,834,033 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,958,700
duplication rate = 47.07%
>>>>>>> Insert size
mean insert size = 20,189.6438
std insert size = 1,396,708.6675
median insert size = 204
>>>>>>> Mapping quality
mean mapping quality = 54.7718
>>>>>>> ACTG content
number of A's = 455,037,352 bp (26.98%)
number of C's = 389,495,952 bp (23.09%)
number of T's = 456,017,099 bp (27.03%)
number of G's = 386,074,033 bp (22.89%)
number of N's = 209,597 bp (0.01%)
GC percentage = 45.98%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 9,001,569
number of insertions = 100,180
mapped reads with insertion percentage = 0.58%
number of deletions = 80,580
mapped reads with deletion percentage = 0.46%
homopolymer indels = 46.2%
>>>>>>> Coverage
mean coverageData = 0.545X
std coverageData = 18.258X
There is a 4.83% of reference with a coverageData >= 1X
There is a 2.17% of reference with a coverageData >= 2X
There is a 0.9% of reference with a coverageData >= 3X
There is a 0.66% of reference with a coverageData >= 4X
There is a 0.48% 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 0.33% 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 0.29% 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 0.27% of reference with a coverageData >= 19X
There is a 0.26% of reference with a coverageData >= 20X
There is a 0.26% of reference with a coverageData >= 21X
There is a 0.25% of reference with a coverageData >= 22X
There is a 0.25% 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 0.23% 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 0.18% 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 0.17% 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 162208380 0.6507842562205692 21.17347702750338
chr2 243199373 155388721 0.6389355329464603 26.189676228385633
chr3 198022430 122819577 0.6202306324591613 14.949474280127836
chr4 191154276 51796437 0.27096666673572084 9.82820047169156
chr5 180915260 75430510 0.41693835003194313 17.5409485705566
chr6 171115067 149513264 0.873758615306506 21.389005817296766
chr7 159138663 100439511 0.6311446200851895 19.09368645499722
chr8 146364022 169542300 1.1583604883446015 33.46442277739516
chr9 141213431 55706261 0.39448273868510425 10.991382250787138
chr10 135534747 32836961 0.24227706714942995 10.071481304296451
chr11 135006516 38380208 0.2842841155903912 9.472960218381411
chr12 133851895 90436837 0.6756485367652061 16.98607986528176
chr13 115169878 70914798 0.6157408450150481 21.80957029419594
chr14 107349540 23993739 0.22351040349124923 6.364519037009831
chr15 102531392 33231194 0.32410750845945796 13.485526510775133
chr16 90354753 68602065 0.7592524213972451 18.0714945992809
chr17 81195210 68617474 0.8450926353906838 20.62657589948374
chr18 78077248 8995955 0.11521864858761416 5.728870393262383
chr19 59128983 24309823 0.4111321008176312 10.2114603573915
chr20 63025520 49433002 0.7843331082393291 18.500114779835318
chr21 48129895 13080055 0.27176570819446 11.44316464614386
chr22 51304566 26763873 0.5216664926080848 19.392870684188885
chrMT 16571 4676 0.2821797115442641 0.6013109201922526
chrX 155270560 94293771 0.607286861076562 18.880461973304264
chrY 59373566 282146 0.0047520474010269145 0.2553425127190188