BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124823.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 30,761,518
number of mapped reads = 30,255,154 (98.35%)
number of supplementary alignments = 136,179 (0.44%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 15,136,887
number of mapped paired reads (second in pair) = 15,118,267
number of mapped paired reads (both in pair) = 30,141,762
number of mapped paired reads (singletons) = 113,392
number of mapped bases = 2,770,003,354 bp
number of sequenced bases = 2,768,425,056 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 3,228,436
duplication rate = 5.82%
>>>>>>> Insert size
mean insert size = 79,407.156
std insert size = 2,696,057.4534
median insert size = 174
>>>>>>> Mapping quality
mean mapping quality = 52.6887
>>>>>>> ACTG content
number of A's = 786,381,766 bp (28.41%)
number of C's = 561,663,431 bp (20.29%)
number of T's = 810,228,080 bp (29.27%)
number of G's = 610,131,024 bp (22.04%)
number of N's = 20,755 bp (0%)
GC percentage = 42.33%
>>>>>>> Mismatches and indels
general error rate = 0.0077
number of mismatches = 20,380,581
number of insertions = 393,208
mapped reads with insertion percentage = 1.27%
number of deletions = 927,201
mapped reads with deletion percentage = 3%
homopolymer indels = 47.54%
>>>>>>> Coverage
mean coverageData = 0.8948X
std coverageData = 8.5914X
There is a 30.59% of reference with a coverageData >= 1X
There is a 18.46% of reference with a coverageData >= 2X
There is a 11.35% of reference with a coverageData >= 3X
There is a 7.32% of reference with a coverageData >= 4X
There is a 4.84% of reference with a coverageData >= 5X
There is a 3.28% of reference with a coverageData >= 6X
There is a 2.28% of reference with a coverageData >= 7X
There is a 1.61% of reference with a coverageData >= 8X
There is a 1.16% of reference with a coverageData >= 9X
There is a 0.85% of reference with a coverageData >= 10X
There is a 0.64% of reference with a coverageData >= 11X
There is a 0.49% of reference with a coverageData >= 12X
There is a 0.38% of reference with a coverageData >= 13X
There is a 0.3% of reference with a coverageData >= 14X
There is a 0.24% of reference with a coverageData >= 15X
There is a 0.2% of reference with a coverageData >= 16X
There is a 0.16% 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 0.06% of reference with a coverageData >= 25X
There is a 0.05% of reference with a coverageData >= 26X
There is a 0.05% of reference with a coverageData >= 27X
There is a 0.05% of reference with a coverageData >= 28X
There is a 0.04% of reference with a coverageData >= 29X
There is a 0.04% of reference with a coverageData >= 30X
There is a 0.04% 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 0.03% of reference with a coverageData >= 35X
There is a 0.03% of reference with a coverageData >= 36X
There is a 0.03% of reference with a coverageData >= 37X
There is a 0.03% 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 0.02% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 232220608 0.9316751431483896 9.307064357692916
chr2 243199373 205772535 0.846106354887683 10.190904713477048
chr3 198022430 264541499 1.3359168403296535 3.1380034929402165
chr4 191154276 161178266 0.8431842037370904 4.935397098537849
chr5 180915260 160913138 0.8894392767088857 2.0037486393663557
chr6 171115067 157946985 0.9230454557224934 10.500078928328243
chr7 159138663 154967126 0.9737867786409642 11.909198036807574
chr8 146364022 186371477 1.2733421400513303 3.62869447488534
chr9 141213431 116955656 0.8282190664994181 12.483432770624223
chr10 135534747 131200531 0.9680213665061108 18.700022534082823
chr11 135006516 135679457 1.0049845075625832 7.996258309061187
chr12 133851895 110206418 0.8233459675710979 1.8366379598899893
chr13 115169878 70674789 0.6136568886527778 1.6858596630272864
chr14 107349540 95943374 0.8937474161510147 2.56501021116597
chr15 102531392 51898815 0.5061748795919985 1.3696411234810837
chr16 90354753 81413326 0.9010408782811902 14.435295698095164
chr17 81195210 58781229 0.723949466969788 7.517984353988983
chr18 78077248 90753759 1.1623585785195707 13.617908362735374
chr19 59128983 62388469 1.055125013734804 5.985073955919677
chr20 63025520 67190514 1.0660842465083984 2.48522127311805
chr21 48129895 33844497 0.7031907507797389 2.7399127847872133
chr22 51304566 26915209 0.5246162495556438 1.711039587238436
chrMT 16571 685899 41.39152736708708 20.991707195436693
chrX 155270560 77800697 0.5010653468371596 3.7533090209072197
chrY 59373566 33759081 0.568587728080877 11.583484158190009