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 |