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 (inside of regions)

Number/percentage of A's 77,753,463 / 36.36%
Number/percentage of C's 29,164,712 / 13.64%
Number/percentage of T's 77,522,187 / 36.25%
Number/percentage of G's 29,430,157 / 13.76%
Number/percentage of N's 0 / 0%
GC Percentage 27.4%

Coverage (inside of regions)

Mean 15.6
Standard Deviation 138.99

Mapping Quality (inside of regions)

Mean Mapping Quality 42.21

Insert size (inside of regions)

Mean 81.77
Median Estimation 1

Per chromosome statistics (inside of regions)

Name Length Mapped bases Mean coverage Standard deviation
MAL1 643292 11465909 35.84 327.59
MAL10 1687655 15828953 16.49 81.73
MAL11 2038337 21220199 17.51 144.81
MAL12 2271477 20585179 15.28 52.69
MAL13 2895605 20438366 11.57 42.22
MAL14 3291871 34105226 16.99 219.82
MAL2 947102 10643889 20.19 106.42
MAL3 1060087 5228770 8.02 33.63
MAL4 1204112 4465238 6.17 23.84
MAL5 1343552 16960522 20.78 188.54
MAL6 1418244 12802513 15.28 93.51
MAL7 1501717 12943630 14.02 216.97
MAL8 1419563 9208669 10.91 65.71
MAL9 1541723 17973456 19.81 66
PF_apicoplast_genome_1 29430 0 0 0
Pf_mito 5967 0 0 0

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