BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1819014.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,265,720
number of mapped reads = 3,069,204 (93.98%)
number of supplementary alignments = 48,160 (1.47%)
number of secondary alignments = 0
number of mapped bases = 283,918,324 bp
number of sequenced bases = 283,747,171 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,572,120
duplication rate = 43.13%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.1244
>>>>>>> ACTG content
number of A's = 82,877,586 bp (29.21%)
number of C's = 59,580,615 bp (21%)
number of T's = 82,051,430 bp (28.92%)
number of G's = 59,223,337 bp (20.87%)
number of N's = 14,203 bp (0.01%)
GC percentage = 41.87%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 1,793,180
number of insertions = 45,987
mapped reads with insertion percentage = 1.46%
number of deletions = 91,970
mapped reads with deletion percentage = 2.93%
homopolymer indels = 40.99%
>>>>>>> Coverage
mean coverageData = 0.0917X
std coverageData = 1.0568X
There is a 3.61% of reference with a coverageData >= 1X
There is a 2% of reference with a coverageData >= 2X
There is a 1.22% of reference with a coverageData >= 3X
There is a 0.76% of reference with a coverageData >= 4X
There is a 0.48% of reference with a coverageData >= 5X
There is a 0.3% of reference with a coverageData >= 6X
There is a 0.19% of reference with a coverageData >= 7X
There is a 0.12% of reference with a coverageData >= 8X
There is a 0.08% of reference with a coverageData >= 9X
There is a 0.05% of reference with a coverageData >= 10X
There is a 0.04% of reference with a coverageData >= 11X
There is a 0.03% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 27769928 0.11141367627725991 1.926610210896565
chr2 243199373 22940272 0.09432701950263662 1.4714424564382316
chr3 198022430 15707046 0.07931952961086276 0.571456992436755
chr4 191154276 15857154 0.08295474384261224 0.6816223636684103
chr5 180915260 15825892 0.08747682202153649 0.6189391004691576
chr6 171115067 12117857 0.07081700759875224 0.6819739621566987
chr7 159138663 13925731 0.0875068995646897 1.2522102246275078
chr8 146364022 26248075 0.17933420140640846 0.9906333028710931
chr9 141213431 12557990 0.08892914725653822 1.0077704671198329
chr10 135534747 14945885 0.1102734562967827 1.347551706079822
chr11 135006516 9551647 0.07074952589695745 0.6881467434022251
chr12 133851895 12421238 0.09279837241004321 0.6351939502933756
chr13 115169878 6014195 0.05222020813463048 0.45824229414263906
chr14 107349540 6752636 0.0629032597624545 0.5512721888746182
chr15 102531392 7559114 0.07372487442675117 0.551255008120632
chr16 90354753 9003176 0.09964252793652151 1.1918195197258288
chr17 81195210 9653172 0.11888844181818115 0.790406053236671
chr18 78077248 6781727 0.08685919616429104 1.1372983609139107
chr19 59128983 5814929 0.09834312557007788 1.7559174820101227
chr20 63025520 8326635 0.1321152923450691 0.8060782464112503
chr21 48129895 3899011 0.08101017049798259 0.6535877401875209
chr22 51304566 2174678 0.04238761127031072 0.46568562398518326
chrMT 16571 50321 3.0366906040673465 4.005093357211271
chrX 155270560 16927705 0.10902069909453536 0.7854254650944646
chrY 59373566 1092310 0.01839724432249867 1.169264292447087