Summary 

Globals

Reference size 23,299,734
Number of selected regions 5,452
Size/percentage of selected regions 13,711,554/58.85%
Size/percentage of non-selected regions 9,588,180/41.15%
Number of reads 8,386,304
Number/percentage of mapped reads 5,830,399 / 69.52%
Number/percentage of mapped reads inside of regions 4,552,567 / 78.08%
Number/percentage of mapped reads outside of regions 1,277,832 / 21.92%
Number/percentage of unmapped reads 2,555,905/30.48%
Number/percentage of paired reads 5,830,399/69.52%
Number/percentage of reads both mates paired 5,245,862/62.55%
Number/percentage of singletons 584,537/6.97%
Read min/max/mean size 12/54/49.65

ACGT Content (outside of regions)

Number/percentage of A's 25,205,877 / 39.18%
Number/percentage of C's 7,353,985 / 11.43%
Number/percentage of T's 24,391,597 / 37.91%
Number/percentage of G's 7,388,859 / 11.48%
Number/percentage of N's 0 / 0%
GC Percentage 22.91%

Coverage (outside of regions)

Mean 4.69
Standard Deviation 66.74

Mapping Quality (outside of regions)

Mean Mapping Quality 39.26

Insert size (outside of regions)

Mean 77.45
Median Estimation 1

Per chromosome statistics (outside of regions)

Name Length Mapped bases Mean coverage Standard deviation
MAL1 643292 1861740 5.71 55.73
MAL10 1687655 3184372 4.37 80.04
MAL11 2038337 6143140 7.43 172.05
MAL12 2271477 3572946 3.87 22.17
MAL13 2895605 8636941 7.65 35.96
MAL14 3291871 5548109 4.32 80.87
MAL2 947102 1410652 3.36 24.23
MAL3 1060087 3858930 8.82 34.08
MAL4 1204112 3664145 7.05 31.82
MAL5 1343552 1823439 3.46 21.64
MAL6 1418244 2014202 3.47 48.12
MAL7 1501717 11505051 18.44 151.8
MAL8 1419563 7993675 13.9 69.33
MAL9 1541723 2524665 3.84 19.55
PF_apicoplast_genome_1 29430 296884 10.09 29.14
Pf_mito 5967 301427 50.52 18.52

Input data and parameters 

Alignment

BAM file: /home/fgarcia/qualimapLatestBuild/dataRelease/genomics/Plasmodium-falciparum-3D7_RNASeq.bam
Number of windows: 400
Analysis date: Tue Apr 24 19:45:34 CEST 2012
Draw chromosome limits: yes

GFF region

GFF file: /home/fgarcia/qualimapLatestBuild/dataRelease/annotations/Plasmodium-falciparum-3D7.gff
Outside statistics: 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