BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472606.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 = 15,087,434
number of mapped reads = 14,971,719 (99.23%)
number of supplementary alignments = 73,927 (0.49%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 7,504,824
number of mapped paired reads (second in pair) = 7,466,895
number of mapped paired reads (both in pair) = 14,892,496
number of mapped paired reads (singletons) = 79,223
number of mapped bases = 1,472,487,022 bp
number of sequenced bases = 1,472,264,775 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,121,501
duplication rate = 49.52%
>>>>>>> Insert size
mean insert size = 20,988.2377
std insert size = 1,446,000.3126
median insert size = 206
>>>>>>> Mapping quality
mean mapping quality = 54.7241
>>>>>>> ACTG content
number of A's = 400,470,653 bp (27.2%)
number of C's = 337,396,020 bp (22.92%)
number of T's = 401,496,710 bp (27.27%)
number of G's = 332,626,876 bp (22.59%)
number of N's = 274,516 bp (0.02%)
GC percentage = 45.51%
>>>>>>> Mismatches and indels
general error rate = 0.0061
number of mismatches = 8,795,838
number of insertions = 90,277
mapped reads with insertion percentage = 0.59%
number of deletions = 80,062
mapped reads with deletion percentage = 0.53%
homopolymer indels = 45.27%
>>>>>>> Coverage
mean coverageData = 0.4757X
std coverageData = 19.6979X
There is a 3.02% of reference with a coverageData >= 1X
There is a 1.42% of reference with a coverageData >= 2X
There is a 0.69% of reference with a coverageData >= 3X
There is a 0.54% of reference with a coverageData >= 4X
There is a 0.42% of reference with a coverageData >= 5X
There is a 0.39% of reference with a coverageData >= 6X
There is a 0.35% of reference with a coverageData >= 7X
There is a 0.33% of reference with a coverageData >= 8X
There is a 0.31% of reference with a coverageData >= 9X
There is a 0.3% of reference with a coverageData >= 10X
There is a 0.29% of reference with a coverageData >= 11X
There is a 0.28% of reference with a coverageData >= 12X
There is a 0.27% of reference with a coverageData >= 13X
There is a 0.26% of reference with a coverageData >= 14X
There is a 0.25% of reference with a coverageData >= 15X
There is a 0.25% of reference with a coverageData >= 16X
There is a 0.24% of reference with a coverageData >= 17X
There is a 0.24% of reference with a coverageData >= 18X
There is a 0.23% of reference with a coverageData >= 19X
There is a 0.22% of reference with a coverageData >= 20X
There is a 0.22% of reference with a coverageData >= 21X
There is a 0.21% of reference with a coverageData >= 22X
There is a 0.21% of reference with a coverageData >= 23X
There is a 0.21% of reference with a coverageData >= 24X
There is a 0.2% of reference with a coverageData >= 25X
There is a 0.2% of reference with a coverageData >= 26X
There is a 0.19% of reference with a coverageData >= 27X
There is a 0.19% of reference with a coverageData >= 28X
There is a 0.19% of reference with a coverageData >= 29X
There is a 0.18% of reference with a coverageData >= 30X
There is a 0.18% of reference with a coverageData >= 31X
There is a 0.18% of reference with a coverageData >= 32X
There is a 0.18% of reference with a coverageData >= 33X
There is a 0.17% of reference with a coverageData >= 34X
There is a 0.17% of reference with a coverageData >= 35X
There is a 0.17% of reference with a coverageData >= 36X
There is a 0.17% of reference with a coverageData >= 37X
There is a 0.16% of reference with a coverageData >= 38X
There is a 0.16% 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 0.15% of reference with a coverageData >= 42X
There is a 0.15% of reference with a coverageData >= 43X
There is a 0.15% 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 0.14% of reference with a coverageData >= 47X
There is a 0.14% of reference with a coverageData >= 48X
There is a 0.14% 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 178589090 0.7165040924812781 25.23500402571093
chr2 243199373 133194774 0.5476772919147287 20.585929742880236
chr3 198022430 129801977 0.6554912844974178 22.2398006650174
chr4 191154276 31955049 0.1671688945111539 10.607797938235198
chr5 180915260 57078341 0.31549765895922766 11.801872182425042
chr6 171115067 121385226 0.7093777779369949 20.865606184128435
chr7 159138663 131717263 0.8276886365445963 28.621589140901236
chr8 146364022 76861405 0.5251386505353071 18.122098166602594
chr9 141213431 53869708 0.38147722648279825 11.478274492207506
chr10 135534747 39185216 0.2891156464843661 15.398613212812469
chr11 135006516 29896665 0.22144608931320026 8.802549905420511
chr12 133851895 35084965 0.26211780565377873 10.330147152811692
chr13 115169878 62124823 0.5394190223940326 28.341009990493056
chr14 107349540 27782144 0.2588007736223183 11.058918424422373
chr15 102531392 11368197 0.11087528198193193 6.053173366508459
chr16 90354753 72109299 0.7980686859937518 24.660413962017476
chr17 81195210 85036479 1.0473090592413026 42.0841687716155
chr18 78077248 8213074 0.10519164302512302 3.5589339016602017
chr19 59128983 43262622 0.7316652478193308 31.020526142661048
chr20 63025520 43756992 0.6942741924223711 20.421941518842573
chr21 48129895 11038293 0.22934379973195454 9.010694350751846
chr22 51304566 16030606 0.3124596356589392 10.311516432988283
chrMT 16571 2749 0.16589222135055218 0.5306923006750102
chrX 155270560 72915151 0.46960061843017764 20.369467621146843
chrY 59373566 226914 0.0038218017762315305 0.24090622014316831