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 |