BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1153365.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 46,735,180
number of mapped reads = 46,432,066 (99.35%)
number of supplementary alignments = 256,510 (0.55%)
number of secondary alignments = 0
number of mapped bases = 4,520,196,428 bp
number of sequenced bases = 4,519,636,153 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 31,140,868
duplication rate = 57.48%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 50.5149
>>>>>>> ACTG content
number of A's = 1,204,642,041 bp (26.65%)
number of C's = 1,047,110,873 bp (23.17%)
number of T's = 1,239,249,302 bp (27.42%)
number of G's = 1,027,316,256 bp (22.73%)
number of N's = 1,317,681 bp (0.03%)
GC percentage = 45.9%
>>>>>>> Mismatches and indels
general error rate = 0.0026
number of mismatches = 11,195,672
number of insertions = 319,798
mapped reads with insertion percentage = 0.68%
number of deletions = 280,804
mapped reads with deletion percentage = 0.6%
homopolymer indels = 49.89%
>>>>>>> Coverage
mean coverageData = 1.4602X
std coverageData = 16.9997X
There is a 10.1% of reference with a coverageData >= 1X
There is a 6.96% of reference with a coverageData >= 2X
There is a 4.59% of reference with a coverageData >= 3X
There is a 3.81% of reference with a coverageData >= 4X
There is a 3% of reference with a coverageData >= 5X
There is a 2.73% of reference with a coverageData >= 6X
There is a 2.39% of reference with a coverageData >= 7X
There is a 2.24% of reference with a coverageData >= 8X
There is a 2.07% of reference with a coverageData >= 9X
There is a 1.96% of reference with a coverageData >= 10X
There is a 1.86% of reference with a coverageData >= 11X
There is a 1.78% of reference with a coverageData >= 12X
There is a 1.7% of reference with a coverageData >= 13X
There is a 1.64% of reference with a coverageData >= 14X
There is a 1.58% of reference with a coverageData >= 15X
There is a 1.53% of reference with a coverageData >= 16X
There is a 1.48% of reference with a coverageData >= 17X
There is a 1.43% of reference with a coverageData >= 18X
There is a 1.39% of reference with a coverageData >= 19X
There is a 1.34% of reference with a coverageData >= 20X
There is a 1.31% of reference with a coverageData >= 21X
There is a 1.27% of reference with a coverageData >= 22X
There is a 1.24% of reference with a coverageData >= 23X
There is a 1.2% of reference with a coverageData >= 24X
There is a 1.17% of reference with a coverageData >= 25X
There is a 1.14% of reference with a coverageData >= 26X
There is a 1.11% of reference with a coverageData >= 27X
There is a 1.09% of reference with a coverageData >= 28X
There is a 1.06% of reference with a coverageData >= 29X
There is a 1.04% of reference with a coverageData >= 30X
There is a 1.01% of reference with a coverageData >= 31X
There is a 0.99% of reference with a coverageData >= 32X
There is a 0.97% of reference with a coverageData >= 33X
There is a 0.95% of reference with a coverageData >= 34X
There is a 0.93% of reference with a coverageData >= 35X
There is a 0.91% of reference with a coverageData >= 36X
There is a 0.89% of reference with a coverageData >= 37X
There is a 0.87% of reference with a coverageData >= 38X
There is a 0.85% of reference with a coverageData >= 39X
There is a 0.84% of reference with a coverageData >= 40X
There is a 0.82% of reference with a coverageData >= 41X
There is a 0.8% of reference with a coverageData >= 42X
There is a 0.79% of reference with a coverageData >= 43X
There is a 0.77% of reference with a coverageData >= 44X
There is a 0.76% of reference with a coverageData >= 45X
There is a 0.75% of reference with a coverageData >= 46X
There is a 0.73% of reference with a coverageData >= 47X
There is a 0.72% of reference with a coverageData >= 48X
There is a 0.71% of reference with a coverageData >= 49X
There is a 0.69% of reference with a coverageData >= 50X
There is a 0.68% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 359765860 1.4433900246932585 14.330227231948893
chr2 243199373 390578273 1.6060003287919662 16.496590898698656
chr3 198022430 278456419 1.4061862537491334 14.521647360887124
chr4 191154276 154016222 0.8057168545892219 10.02181490128082
chr5 180915260 271790024 1.5023056872040534 17.00131104673191
chr6 171115067 194251829 1.1352117169202873 12.825139769669944
chr7 159138663 238563583 1.4990925429604747 16.711564871033175
chr8 146364022 279015685 1.9063133219993094 32.38995563731464
chr9 141213431 119033086 0.8429303442106721 10.13855744428849
chr10 135534747 234869707 1.7329113913497032 17.800681017274623
chr11 135006516 221168419 1.638205514465687 15.319073107906293
chr12 133851895 208664414 1.5589201333309477 14.978648860420382
chr13 115169878 58607896 0.5088821575377548 8.069219665974787
chr14 107349540 105616875 0.9838595954859238 10.508209882222888
chr15 102531392 149708365 1.460122232613403 13.488284426710573
chr16 90354753 201574649 2.230924686385895 22.51012170335905
chr17 81195210 189985955 2.339866538925141 18.6454265705617
chr18 78077248 41439802 0.5307538759562838 7.536546811438953
chr19 59128983 201696485 3.411127247021989 28.020266227849337
chr20 63025520 108243784 1.7174595941453557 16.864188472106395
chr21 48129895 45368573 0.9426277161003571 11.122876104754333
chr22 51304566 61217256 1.1932126275076569 12.791340055062493
chrMT 16571 26517 1.6002051777201134 5.610821723345683
chrX 155270560 402950851 2.5951529446406325 28.043739331245355
chrY 59373566 3585899 0.06039554706887573 2.403100101522971