BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472742.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 = 14,295,066
number of mapped reads = 14,139,648 (98.91%)
number of supplementary alignments = 70,074 (0.49%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 7,099,519
number of mapped paired reads (second in pair) = 7,040,129
number of mapped paired reads (both in pair) = 14,046,812
number of mapped paired reads (singletons) = 92,836
number of mapped bases = 1,394,631,777 bp
number of sequenced bases = 1,394,434,426 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,702,086
duplication rate = 45.39%
>>>>>>> Insert size
mean insert size = 29,518.1527
std insert size = 1,672,156.4614
median insert size = 249
>>>>>>> Mapping quality
mean mapping quality = 54.9293
>>>>>>> ACTG content
number of A's = 385,384,698 bp (27.64%)
number of C's = 313,971,083 bp (22.52%)
number of T's = 383,327,109 bp (27.49%)
number of G's = 311,482,926 bp (22.34%)
number of N's = 268,610 bp (0.02%)
GC percentage = 44.85%
>>>>>>> Mismatches and indels
general error rate = 0.0064
number of mismatches = 8,790,051
number of insertions = 92,634
mapped reads with insertion percentage = 0.65%
number of deletions = 80,344
mapped reads with deletion percentage = 0.56%
homopolymer indels = 46.05%
>>>>>>> Coverage
mean coverageData = 0.4505X
std coverageData = 16.2797X
There is a 4.18% of reference with a coverageData >= 1X
There is a 1.79% of reference with a coverageData >= 2X
There is a 0.83% of reference with a coverageData >= 3X
There is a 0.61% of reference with a coverageData >= 4X
There is a 0.47% of reference with a coverageData >= 5X
There is a 0.42% of reference with a coverageData >= 6X
There is a 0.38% of reference with a coverageData >= 7X
There is a 0.36% of reference with a coverageData >= 8X
There is a 0.34% of reference with a coverageData >= 9X
There is a 0.33% of reference with a coverageData >= 10X
There is a 0.31% of reference with a coverageData >= 11X
There is a 0.3% of reference with a coverageData >= 12X
There is a 0.29% of reference with a coverageData >= 13X
There is a 0.28% of reference with a coverageData >= 14X
There is a 0.27% of reference with a coverageData >= 15X
There is a 0.26% of reference with a coverageData >= 16X
There is a 0.26% of reference with a coverageData >= 17X
There is a 0.25% of reference with a coverageData >= 18X
There is a 0.24% of reference with a coverageData >= 19X
There is a 0.24% of reference with a coverageData >= 20X
There is a 0.23% of reference with a coverageData >= 21X
There is a 0.23% of reference with a coverageData >= 22X
There is a 0.22% of reference with a coverageData >= 23X
There is a 0.22% of reference with a coverageData >= 24X
There is a 0.21% of reference with a coverageData >= 25X
There is a 0.21% of reference with a coverageData >= 26X
There is a 0.2% of reference with a coverageData >= 27X
There is a 0.2% of reference with a coverageData >= 28X
There is a 0.2% of reference with a coverageData >= 29X
There is a 0.19% of reference with a coverageData >= 30X
There is a 0.19% of reference with a coverageData >= 31X
There is a 0.19% of reference with a coverageData >= 32X
There is a 0.18% of reference with a coverageData >= 33X
There is a 0.18% of reference with a coverageData >= 34X
There is a 0.18% of reference with a coverageData >= 35X
There is a 0.18% of reference with a coverageData >= 36X
There is a 0.17% of reference with a coverageData >= 37X
There is a 0.17% of reference with a coverageData >= 38X
There is a 0.17% of reference with a coverageData >= 39X
There is a 0.16% of reference with a coverageData >= 40X
There is a 0.16% of reference with a coverageData >= 41X
There is a 0.16% of reference with a coverageData >= 42X
There is a 0.16% of reference with a coverageData >= 43X
There is a 0.16% of reference with a coverageData >= 44X
There is a 0.15% of reference with a coverageData >= 45X
There is a 0.15% of reference with a coverageData >= 46X
There is a 0.15% of reference with a coverageData >= 47X
There is a 0.15% of reference with a coverageData >= 48X
There is a 0.15% of reference with a coverageData >= 49X
There is a 0.14% of reference with a coverageData >= 50X
There is a 0.14% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 133036090 0.5337442669801814 17.81217129167895
chr2 243199373 82435023 0.3389606724027204 11.268264830346979
chr3 198022430 168082324 0.8488044712914593 20.97538000057901
chr4 191154276 57058001 0.298491889347011 11.416005970120343
chr5 180915260 53319524 0.29472098705217015 8.758266675195596
chr6 171115067 80081794 0.4679996648103466 14.264059244011788
chr7 159138663 61330543 0.3853905885837435 16.022734609626422
chr8 146364022 58886929 0.4023319952221592 15.324268948634769
chr9 141213431 103595399 0.7336086820240207 23.22943701481017
chr10 135534747 42681681 0.3149132008192704 14.169864959801048
chr11 135006516 66723144 0.49422165667914875 16.820988627364525
chr12 133851895 89023091 0.6650865196940245 27.978562468424943
chr13 115169878 49192936 0.42713369896944753 21.254094055174356
chr14 107349540 31745187 0.2957179602260056 10.093200639867366
chr15 102531392 24861172 0.2424737586709054 8.062037554363359
chr16 90354753 48107927 0.5324338278031705 14.649547349010215
chr17 81195210 67913957 0.8364281218066928 23.618286733412983
chr18 78077248 28716337 0.36779391865860844 16.067868136907258
chr19 59128983 27311335 0.4618942118453145 11.706711898689331
chr20 63025520 35010931 0.5555040402681326 19.32576224702572
chr21 48129895 6039575 0.12548489873082 5.081075168679674
chr22 51304566 12937829 0.2521769504881885 6.086482729565426
chrMT 16571 2252 0.13590006638102708 0.4862451192602978
chrX 155270560 63979391 0.4120510095410231 15.769879593649618
chrY 59373566 2559405 0.04310680951856589 1.7014631570597287