BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR617647.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000
number of mapped reads = 30,191,074 (94.35%)
number of supplementary alignments = 143,380 (0.45%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 15,160,210
number of mapped paired reads (second in pair) = 15,030,864
number of mapped paired reads (both in pair) = 29,659,108
number of mapped paired reads (singletons) = 531,966
number of mapped bases = 2,932,252,903 bp
number of sequenced bases = 2,930,479,643 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 6,904,238
duplication rate = 10.66%
>>>>>>> Insert size
mean insert size = 32,667.9821
std insert size = 1,659,122.611
median insert size = 222
>>>>>>> Mapping quality
mean mapping quality = 52.6642
>>>>>>> ACTG content
number of A's = 873,424,345 bp (29.8%)
number of C's = 583,905,399 bp (19.93%)
number of T's = 871,389,493 bp (29.74%)
number of G's = 599,664,772 bp (20.46%)
number of N's = 2,095,634 bp (0.07%)
GC percentage = 40.39%
>>>>>>> Mismatches and indels
general error rate = 0.0153
number of mismatches = 43,879,061
number of insertions = 454,846
mapped reads with insertion percentage = 1.48%
number of deletions = 1,071,812
mapped reads with deletion percentage = 3.48%
homopolymer indels = 47.71%
>>>>>>> Coverage
mean coverageData = 0.9472X
std coverageData = 10.6891X
There is a 33.27% of reference with a coverageData >= 1X
There is a 19.27% of reference with a coverageData >= 2X
There is a 11.77% of reference with a coverageData >= 3X
There is a 7.51% of reference with a coverageData >= 4X
There is a 4.94% of reference with a coverageData >= 5X
There is a 3.35% of reference with a coverageData >= 6X
There is a 2.32% of reference with a coverageData >= 7X
There is a 1.65% of reference with a coverageData >= 8X
There is a 1.19% of reference with a coverageData >= 9X
There is a 0.88% of reference with a coverageData >= 10X
There is a 0.66% of reference with a coverageData >= 11X
There is a 0.51% of reference with a coverageData >= 12X
There is a 0.39% of reference with a coverageData >= 13X
There is a 0.31% of reference with a coverageData >= 14X
There is a 0.25% of reference with a coverageData >= 15X
There is a 0.2% of reference with a coverageData >= 16X
There is a 0.17% of reference with a coverageData >= 17X
There is a 0.14% of reference with a coverageData >= 18X
There is a 0.12% of reference with a coverageData >= 19X
There is a 0.1% of reference with a coverageData >= 20X
There is a 0.09% of reference with a coverageData >= 21X
There is a 0.08% of reference with a coverageData >= 22X
There is a 0.07% of reference with a coverageData >= 23X
There is a 0.06% of reference with a coverageData >= 24X
There is a 0.05% of reference with a coverageData >= 25X
There is a 0.05% of reference with a coverageData >= 26X
There is a 0.04% of reference with a coverageData >= 27X
There is a 0.04% of reference with a coverageData >= 28X
There is a 0.04% of reference with a coverageData >= 29X
There is a 0.03% of reference with a coverageData >= 30X
There is a 0.03% of reference with a coverageData >= 31X
There is a 0.03% of reference with a coverageData >= 32X
There is a 0.03% of reference with a coverageData >= 33X
There is a 0.03% of reference with a coverageData >= 34X
There is a 0.02% of reference with a coverageData >= 35X
There is a 0.02% of reference with a coverageData >= 36X
There is a 0.02% of reference with a coverageData >= 37X
There is a 0.02% of reference with a coverageData >= 38X
There is a 0.02% of reference with a coverageData >= 39X
There is a 0.02% of reference with a coverageData >= 40X
There is a 0.02% of reference with a coverageData >= 41X
There is a 0.02% of reference with a coverageData >= 42X
There is a 0.02% of reference with a coverageData >= 43X
There is a 0.02% of reference with a coverageData >= 44X
There is a 0.02% of reference with a coverageData >= 45X
There is a 0.02% of reference with a coverageData >= 46X
There is a 0.02% of reference with a coverageData >= 47X
There is a 0.02% of reference with a coverageData >= 48X
There is a 0.02% of reference with a coverageData >= 49X
There is a 0.02% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 179623565 0.7206544331939698 10.24378504135641
chr2 243199373 302967772 1.2457588531694117 12.253277653629581
chr3 198022430 246076915 1.2426719286294992 2.4672205782780283
chr4 191154276 164034127 0.8581242880488846 8.412981865044445
chr5 180915260 193977151 1.0721989455173655 2.3222526830732657
chr6 171115067 142116573 0.8305321997156452 5.785883752213832
chr7 159138663 229472261 1.441964238445311 13.496989898559157
chr8 146364022 130658149 0.8926930758981193 4.17410041427972
chr9 141213431 120527263 0.8535113278282999 20.68932735006447
chr10 135534747 124363137 0.9175738307166353 21.80757154214911
chr11 135006516 161150022 1.1936462533408387 12.048039846250909
chr12 133851895 125206992 0.935414414566189 2.1394051994876344
chr13 115169878 125991414 1.0939615130963323 2.287908459176094
chr14 107349540 83920614 0.7817510349834754 2.4693795961112284
chr15 102531392 62481340 0.6093874157097174 1.5706406038401421
chr16 90354753 81250090 0.8992342660712049 16.909462705611208
chr17 81195210 72080938 0.8877486492121888 12.826176985956353
chr18 78077248 54227983 0.6945427046813946 18.369747431322743
chr19 59128983 30909324 0.5227440492254027 6.146392239110921
chr20 63025520 78942132 1.2525423352318235 3.0471156123360905
chr21 48129895 42916636 0.8916835575893112 4.372149695451121
chr22 51304566 18714777 0.3647780004610116 1.2678255772794915
chrMT 16571 3098020 186.95431778408062 132.00814419107522
chrX 155270560 145782042 0.938890424559556 4.3067900054661665
chrY 59373566 11763666 0.1981296861973896 17.477028965410124