BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1505957.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 = 5,630,871
number of mapped reads = 3,969,229 (70.49%)
number of supplementary alignments = 182 (0%)
number of secondary alignments = 0
number of mapped bases = 183,704,953 bp
number of sequenced bases = 183,667,112 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 167,568
duplication rate = 3.11%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9347
>>>>>>> ACTG content
number of A's = 54,188,113 bp (29.5%)
number of C's = 37,856,900 bp (20.61%)
number of T's = 53,512,871 bp (29.14%)
number of G's = 38,108,680 bp (20.75%)
number of N's = 548 bp (0%)
GC percentage = 41.36%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 899,260
number of insertions = 7,907
mapped reads with insertion percentage = 0.2%
number of deletions = 26,911
mapped reads with deletion percentage = 0.68%
homopolymer indels = 46.49%
>>>>>>> Coverage
mean coverageData = 0.0593X
std coverageData = 0.5662X
There is a 4.96% of reference with a coverageData >= 1X
There is a 0.71% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% 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 19713665 0.07909173875237807 1.3751358802551574
chr2 243199373 11126319 0.045749784889453644 0.38749862702684035
chr3 198022430 12043107 0.06081688321873436 0.28769365845349143
chr4 191154276 8387178 0.04387648644595322 0.24415161643490269
chr5 180915260 10914733 0.06033063766981293 0.28751685655646436
chr6 171115067 13160600 0.07691081931435062 0.3700244210911728
chr7 159138663 12654540 0.07951895385724084 0.7930354927909087
chr8 146364022 11776391 0.08045960229215346 0.7139369702860282
chr9 141213431 5226183 0.03700910715780286 0.3181971104203291
chr10 135534747 6146437 0.045349529445759026 0.5812648104115502
chr11 135006516 10352165 0.0766790026638418 0.4720409622893499
chr12 133851895 5282161 0.03946272856278949 0.24127672043023837
chr13 115169878 5445901 0.04728581027063344 0.2467291272321743
chr14 107349540 7088365 0.06603069747667294 0.3321981154123587
chr15 102531392 3348249 0.03265584261257274 0.20607738919132193
chr16 90354753 6342148 0.0701916367365865 0.37497372806447893
chr17 81195210 3186811 0.039248756176626674 0.25835472836098194
chr18 78077248 4817651 0.06170364764905648 0.5742533734542783
chr19 59128983 4870597 0.08237241286561617 0.8557826773732626
chr20 63025520 4562882 0.07239737173132407 0.3129725579840666
chr21 48129895 2825954 0.05871514990838854 0.29578341919908996
chr22 51304566 1342346 0.026164259921816705 0.18669096476572922
chrMT 16571 7923 0.47812443425261 0.8795279957728995
chrX 155270560 12533972 0.08072342883287083 0.3686263760238122
chrY 59373566 548675 0.009241065291581104 0.13980089625674635