Summary 

Globals

Reference size 100,286,002
Number of reads 35,576,180
Mapped reads 30,983,200 / 87.09%
Unmapped reads 4,592,980 / 12.91%
Paired reads 30,983,200 / 87.09%
Mapped reads, only first in pair 15,491,600 / 43.54%
Mapped reads, only second in pair 15,491,600 / 43.54%
Mapped reads, both in pair 30,983,200 / 87.09%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 100 / 100 / 100
Clipped reads 0 / 0%
Duplication rate 16.39%

ACGT Content

Number/percentage of A's 1,003,585,776 / 32.43%
Number/percentage of C's 541,692,060 / 17.5%
Number/percentage of T's 1,006,351,599 / 32.52%
Number/percentage of G's 543,136,344 / 17.55%
Number/percentage of N's 0 / 0%
GC Percentage 35.05%

Coverage

Mean 30.86
Standard Deviation 25.01

Mapping Quality

Mean Mapping Quality 255

Insert size

Mean 407.73
Median 400

Per chromosome statistics

Name Length Mapped bases Mean coverage Standard deviation
I 15072421 467401058 31.01 36.49
II 15279324 456673231 29.89 9.13
III 13783682 416692735 30.23 9.81
IV 17493784 545502943 31.18 10.46
V 20924143 635041765 30.35 18.85
X 17718854 553489637 31.24 8.75
MtDNA 13794 19964410 1,447.33 346.72

Input data and parameters 

Alignment

BAM file: /home/kokonech/qualimap_release_data/alignments/ERR089819.bam
Program: Bowtie (0.12.7)
Command line: "bowtie -S -m 1 -k 1 -p 16 -X 3000 --fr --chunkmbs 2056 /data/scratch/ebwts/c_elegans_ws200 -1 ERR089819_1.fastq -2 ERR089819_2.fastq"
Number of windows: 400
Analysis date: Tue Jul 24 12:04:58 CEST 2012
Draw chromosome limits: yes

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Duplication Rate Histogram 

Genome Fraction Coverage 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram