Summary 

Globals

Reference size 23,264,337
Number of reads 6,649,159
Number/percentage of mapped reads 6,481,948 / 97.49%
Number/percentage of unmapped reads 167,211/2.51%
Number/percentage of paired reads 6,481,948/97.49%
Number/percentage of reads both mates paired 6,442,507/96.89%
Number/percentage of singletons 39,441/0.59%
Read min/max/mean size 76/76/76

ACGT Content

Number/percentage of A's 193,766,502 / 39.6%
Number/percentage of C's 50,669,578 / 10.36%
Number/percentage of T's 193,981,319 / 39.65%
Number/percentage of G's 50,870,741 / 10.4%
Number/percentage of N's 0 / 0%
GC Percentage 20.75%

Coverage

Mean 21.03
Standard Deviation 10

Mapping Quality

Mean Mapping Quality 53.73

Insert size

Mean 177.13
Median Estimation 354

Per chromosome statistics

Name Length Mapped bases Mean coverage Standard deviation
MAL1 643292 14156303 22.01 10.1
MAL2 947102 19638269 20.74 9.71
MAL3 1060087 23125362 21.81 9.83
MAL4 1204112 26691925 22.17 13.5
MAL5 1343552 28354233 21.1 9.95
MAL6 1418244 30426474 21.45 9.91
MAL7 1501717 32782891 21.83 9.55
MAL8 1419563 29538054 20.81 9.62
MAL9 1541723 31382882 20.36 9.71
MAL10 1687655 35633830 21.11 10.2
MAL11 2038337 41616969 20.42 9.52
MAL12 2271477 47845286 21.06 10.07
MAL13 2895605 60752044 20.98 9.67
MAL14 3291871 67343618 20.46 9.46

Input data and parameters 

Alignment

BAM file: /home/fgarcia/qualimapLatestBuild/dataRelease/genomics/Plasmodium-falciparum-3D7.bam
Program: RTA (1.8.70.0)
Number of windows: 400
Analysis date: Tue Apr 24 19:44:07 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