BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549109.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,604,583
number of mapped reads = 10,024,114 (86.38%)
number of secondary alignments = 0
number of mapped bases = 396,803,549 bp
number of sequenced bases = 396,759,799 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 496,078
duplication rate = 3.97%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 41.1357
>>>>>>> ACTG content
number of A's = 110,683,234 bp (27.9%)
number of C's = 87,586,719 bp (22.08%)
number of T's = 110,891,416 bp (27.95%)
number of G's = 87,596,880 bp (22.08%)
number of N's = 1,550 bp (0%)
GC percentage = 44.15%
>>>>>>> Mismatches and indels
general error rate = 0.0034
number of mismatches = 1,322,011
number of insertions = 13,068
mapped reads with insertion percentage = 0.13%
number of deletions = 34,903
mapped reads with deletion percentage = 0.35%
homopolymer indels = 45.69%
>>>>>>> Coverage
mean coverageData = 0.1282X
std coverageData = 0.6932X
There is a 9.25% of reference with a coverageData >= 1X
There is a 2.33% of reference with a coverageData >= 2X
There is a 0.7% of reference with a coverageData >= 3X
There is a 0.24% of reference with a coverageData >= 4X
There is a 0.09% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 33293472 0.1335742790386067 1.0685928601117893
chr2 243199373 33043567 0.13587028038925084 0.7077129237399638
chr3 198022430 25723254 0.12990070872274417 0.4785524090454885
chr4 191154276 22733576 0.11892789675288247 0.47281368987397754
chr5 180915260 23198764 0.12823000116186992 0.48996028736096214
chr6 171115067 22007660 0.12861322141784276 0.5240049171747583
chr7 159138663 22414522 0.14084900285985186 0.8963491415300149
chr8 146364022 19684753 0.13449174688572033 0.9880017841290162
chr9 141213431 17207285 0.12185303393697729 0.6871887431350336
chr10 135534747 19720808 0.14550370614555394 0.6336297194368117
chr11 135006516 18563456 0.1375004447933461 0.6104133485946829
chr12 133851895 18461021 0.13792125244099085 0.5173123697959546
chr13 115169878 11555282 0.10033250187171337 0.41514174036864215
chr14 107349540 12304331 0.1146193174185935 0.6430668867876588
chr15 102531392 12516477 0.12207458375284713 0.4586275981525748
chr16 90354753 13645567 0.151022127192357 0.5501819438826212
chr17 81195210 13654201 0.16816510481344898 0.5552689095595119
chr18 78077248 10183560 0.1304292897208672 1.2630091357512356
chr19 59128983 10797290 0.18260571131419595 1.095513739396319
chr20 63025520 9618920 0.15261944685264 0.5495225684442134
chr21 48129895 5307305 0.11027044625798581 0.5255221406895446
chr22 51304566 6439783 0.12552066028587008 0.5116420526774473
chrMT 16571 168460 10.16595256773882 14.613794421816117
chrX 155270560 11950777 0.076967436711763 0.4560606170580726
chrY 59373566 2609458 0.04394982777352467 0.32452280584696225