BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472699.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 = 14,664,150
number of mapped reads = 14,533,314 (99.11%)
number of supplementary alignments = 24,399 (0.17%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 7,308,069
number of mapped paired reads (second in pair) = 7,225,245
number of mapped paired reads (both in pair) = 14,442,770
number of mapped paired reads (singletons) = 90,544
number of mapped bases = 1,437,949,497 bp
number of sequenced bases = 1,437,743,951 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,593,938
duplication rate = 46.31%
>>>>>>> Insert size
mean insert size = 21,695.7221
std insert size = 1,480,928.0624
median insert size = 240
>>>>>>> Mapping quality
mean mapping quality = 54.863
>>>>>>> ACTG content
number of A's = 390,789,230 bp (27.18%)
number of C's = 327,294,720 bp (22.76%)
number of T's = 398,493,794 bp (27.72%)
number of G's = 320,837,454 bp (22.32%)
number of N's = 328,753 bp (0.02%)
GC percentage = 45.08%
>>>>>>> Mismatches and indels
general error rate = 0.0047
number of mismatches = 6,576,869
number of insertions = 68,359
mapped reads with insertion percentage = 0.46%
number of deletions = 81,583
mapped reads with deletion percentage = 0.55%
homopolymer indels = 44.52%
>>>>>>> Coverage
mean coverageData = 0.4645X
std coverageData = 9.3751X
There is a 3.25% of reference with a coverageData >= 1X
There is a 1.39% of reference with a coverageData >= 2X
There is a 0.78% of reference with a coverageData >= 3X
There is a 0.68% of reference with a coverageData >= 4X
There is a 0.6% of reference with a coverageData >= 5X
There is a 0.57% of reference with a coverageData >= 6X
There is a 0.54% of reference with a coverageData >= 7X
There is a 0.52% of reference with a coverageData >= 8X
There is a 0.5% of reference with a coverageData >= 9X
There is a 0.49% of reference with a coverageData >= 10X
There is a 0.48% of reference with a coverageData >= 11X
There is a 0.46% of reference with a coverageData >= 12X
There is a 0.45% of reference with a coverageData >= 13X
There is a 0.44% of reference with a coverageData >= 14X
There is a 0.43% of reference with a coverageData >= 15X
There is a 0.42% of reference with a coverageData >= 16X
There is a 0.41% of reference with a coverageData >= 17X
There is a 0.41% of reference with a coverageData >= 18X
There is a 0.4% of reference with a coverageData >= 19X
There is a 0.39% of reference with a coverageData >= 20X
There is a 0.38% of reference with a coverageData >= 21X
There is a 0.38% of reference with a coverageData >= 22X
There is a 0.37% of reference with a coverageData >= 23X
There is a 0.36% of reference with a coverageData >= 24X
There is a 0.36% of reference with a coverageData >= 25X
There is a 0.35% of reference with a coverageData >= 26X
There is a 0.35% of reference with a coverageData >= 27X
There is a 0.34% of reference with a coverageData >= 28X
There is a 0.33% of reference with a coverageData >= 29X
There is a 0.33% of reference with a coverageData >= 30X
There is a 0.32% of reference with a coverageData >= 31X
There is a 0.32% of reference with a coverageData >= 32X
There is a 0.31% of reference with a coverageData >= 33X
There is a 0.31% of reference with a coverageData >= 34X
There is a 0.3% of reference with a coverageData >= 35X
There is a 0.3% of reference with a coverageData >= 36X
There is a 0.3% of reference with a coverageData >= 37X
There is a 0.29% of reference with a coverageData >= 38X
There is a 0.29% of reference with a coverageData >= 39X
There is a 0.28% of reference with a coverageData >= 40X
There is a 0.28% of reference with a coverageData >= 41X
There is a 0.27% of reference with a coverageData >= 42X
There is a 0.27% of reference with a coverageData >= 43X
There is a 0.27% of reference with a coverageData >= 44X
There is a 0.26% of reference with a coverageData >= 45X
There is a 0.26% of reference with a coverageData >= 46X
There is a 0.26% of reference with a coverageData >= 47X
There is a 0.25% of reference with a coverageData >= 48X
There is a 0.25% of reference with a coverageData >= 49X
There is a 0.24% of reference with a coverageData >= 50X
There is a 0.24% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 163467393 0.6558354492525016 11.624051113576167
chr2 243199373 102477761 0.4213734588863434 9.277979382568166
chr3 198022430 126257004 0.6375894084321659 10.191375834114499
chr4 191154276 50440917 0.26387543117267226 7.238610057792198
chr5 180915260 67953965 0.3756121235986395 8.320682581538644
chr6 171115067 100576797 0.5877728873518777 9.965214047453085
chr7 159138663 86148403 0.541341754266215 11.263346874520881
chr8 146364022 79408808 0.5425432214482326 10.032571399527594
chr9 141213431 70605255 0.49998965749936347 8.72795209287711
chr10 135534747 36080534 0.26620873833925407 6.470079789751645
chr11 135006516 54441455 0.40325057347602394 8.633345257576716
chr12 133851895 65079863 0.48620800624451377 8.366564432833025
chr13 115169878 37138621 0.3224681804386387 8.816659844251584
chr14 107349540 37895472 0.3530101013940069 7.960851761907396
chr15 102531392 31078261 0.30310971492516164 6.867103001210557
chr16 90354753 78758288 0.871656281324791 16.07235722836056
chr17 81195210 73093687 0.9002216633222575 13.694321837558741
chr18 78077248 21446387 0.2746816460539183 6.06416352875713
chr19 59128983 42352906 0.7162799671355755 9.751404038499858
chr20 63025520 32220903 0.5112358136830922 9.843196248738504
chr21 48129895 11218166 0.23308104038041222 9.743949969633968
chr22 51304566 24543877 0.4783955681449483 9.789834629659868
chrMT 16571 76913 4.64142176090761 3.0277746726309664
chrX 155270560 42680958 0.27488120091793317 4.495678537270801
chrY 59373566 2506903 0.04222254395162992 1.3493115314861996