BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1153318.sorted.bam
outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 102,650,784
number of mapped reads = 99,985,242 (97.4%)
number of supplementary alignments = 608,119 (0.59%)
number of secondary alignments = 0
number of mapped bases = 9,827,951,264 bp
number of sequenced bases = 9,826,277,404 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 47,085,401
duplication rate = 31.27%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.3032
>>>>>>> ACTG content
number of A's = 2,509,039,245 bp (25.53%)
number of C's = 2,403,053,469 bp (24.46%)
number of T's = 2,530,950,946 bp (25.76%)
number of G's = 2,381,333,742 bp (24.23%)
number of N's = 1,900,002 bp (0.02%)
GC percentage = 48.69%
>>>>>>> Mismatches and indels
general error rate = 0.0038
number of mismatches = 36,727,876
number of insertions = 578,784
mapped reads with insertion percentage = 0.57%
number of deletions = 760,268
mapped reads with deletion percentage = 0.75%
homopolymer indels = 45.66%
>>>>>>> Coverage
mean coverageData = 3.1747X
std coverageData = 25.0237X
There is a 47.85% of reference with a coverageData >= 1X
There is a 28.97% of reference with a coverageData >= 2X
There is a 17.88% of reference with a coverageData >= 3X
There is a 12.16% of reference with a coverageData >= 4X
There is a 8.92% of reference with a coverageData >= 5X
There is a 7.04% of reference with a coverageData >= 6X
There is a 5.88% of reference with a coverageData >= 7X
There is a 5.11% of reference with a coverageData >= 8X
There is a 4.58% of reference with a coverageData >= 9X
There is a 4.18% of reference with a coverageData >= 10X
There is a 3.87% of reference with a coverageData >= 11X
There is a 3.63% of reference with a coverageData >= 12X
There is a 3.42% of reference with a coverageData >= 13X
There is a 3.24% of reference with a coverageData >= 14X
There is a 3.09% of reference with a coverageData >= 15X
There is a 2.95% of reference with a coverageData >= 16X
There is a 2.82% of reference with a coverageData >= 17X
There is a 2.71% of reference with a coverageData >= 18X
There is a 2.61% of reference with a coverageData >= 19X
There is a 2.51% of reference with a coverageData >= 20X
There is a 2.42% of reference with a coverageData >= 21X
There is a 2.34% of reference with a coverageData >= 22X
There is a 2.26% of reference with a coverageData >= 23X
There is a 2.18% of reference with a coverageData >= 24X
There is a 2.12% of reference with a coverageData >= 25X
There is a 2.05% of reference with a coverageData >= 26X
There is a 1.99% of reference with a coverageData >= 27X
There is a 1.93% of reference with a coverageData >= 28X
There is a 1.87% of reference with a coverageData >= 29X
There is a 1.82% of reference with a coverageData >= 30X
There is a 1.77% of reference with a coverageData >= 31X
There is a 1.72% of reference with a coverageData >= 32X
There is a 1.67% of reference with a coverageData >= 33X
There is a 1.63% of reference with a coverageData >= 34X
There is a 1.59% of reference with a coverageData >= 35X
There is a 1.55% of reference with a coverageData >= 36X
There is a 1.51% of reference with a coverageData >= 37X
There is a 1.47% of reference with a coverageData >= 38X
There is a 1.43% of reference with a coverageData >= 39X
There is a 1.4% of reference with a coverageData >= 40X
There is a 1.37% of reference with a coverageData >= 41X
There is a 1.33% of reference with a coverageData >= 42X
There is a 1.3% of reference with a coverageData >= 43X
There is a 1.27% of reference with a coverageData >= 44X
There is a 1.25% of reference with a coverageData >= 45X
There is a 1.22% of reference with a coverageData >= 46X
There is a 1.19% of reference with a coverageData >= 47X
There is a 1.16% of reference with a coverageData >= 48X
There is a 1.14% of reference with a coverageData >= 49X
There is a 1.12% of reference with a coverageData >= 50X
There is a 1.09% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 915994674 3.6749945509664346 21.729712464297272
chr2 243199373 559195888 2.2993311253314785 12.731623118148299
chr3 198022430 455545997 2.300476754072758 12.69579438449652
chr4 191154276 323224286 1.6909079554150281 16.70966845127714
chr5 180915260 624348936 3.451057340326073 50.2229019731808
chr6 171115067 269171017 1.573041005208501 10.530302525530631
chr7 159138663 503554242 3.164248288299368 29.820685542129613
chr8 146364022 612745261 4.186447274590472 47.59024851577078
chr9 141213431 259797349 1.8397495702798978 10.772428513049853
chr10 135534747 495932019 3.659076583512566 20.114009122690884
chr11 135006516 434594689 3.2190645450031465 15.101045144168005
chr12 133851895 435983367 3.257207281226762 16.40134529449858
chr13 115169878 111793487 0.9706833847648949 5.87079906206536
chr14 107349540 247554096 2.306056420921785 13.012907823126504
chr15 102531392 507935045 4.953946641044335 27.637714315509452
chr16 90354753 564123554 6.243429761796814 37.77925719016388
chr17 81195210 521460694 6.422308581996401 30.538640601292066
chr18 78077248 104428488 1.3375021619614462 10.736378190617371
chr19 59128983 665101029 11.248308278868926 45.28006082199265
chr20 63025520 296316491 4.701531871533944 21.899050812155114
chr21 48129895 124428668 2.585267804968201 24.63945029443081
chr22 51304566 254904471 4.96845584854962 31.00682061998509
chrMT 16571 217109 13.101744010620964 5.0800799109996015
chrX 155270560 527983698 3.400410857022735 18.199924480014353
chrY 59373566 11616709 0.19565456115605387 8.992808522420788