BAM QC tool from QualiMap (
http://qualimap.org) provides a coverage
plot. See example output here:
http://qualimap.bioinfo.cipf.es/samples/ERR089819_result/qualimapReport.html
This is a QC tool for BAM files.
(likewise, fastQC is a QC tool for fastQ files)
Summary
Globals
| Reference size |
100,286,002 |
| Number of reads |
35,576,180 |
| Mapped reads |
30,983,200 / 87.09% |
| Unmapped reads |
4,592,980 / 12.91% |
| Paired reads |
30,983,200 / 87.09% |
| Mapped reads, only first in pair |
15,491,600 / 43.54% |
| Mapped reads, only second in pair |
15,491,600 / 43.54% |
| Mapped reads, both in pair |
30,983,200 / 87.09% |
| Mapped reads, singletons |
0 / 0% |
| Read min/max/mean length |
100 / 100 / 100 |
| Clipped reads |
0 / 0% |
| Duplication rate |
16.39% |
ACGT Content
| Number/percentage of A's |
1,003,585,776 / 32.43% |
| Number/percentage of C's |
541,692,060 / 17.5% |
| Number/percentage of T's |
1,006,351,599 / 32.52% |
| Number/percentage of G's |
543,136,344 / 17.55% |
| Number/percentage of N's |
0 / 0% |
| GC Percentage |
35.05% |
Coverage
| Mean |
30.86 |
| Standard Deviation |
25.01 |
Per chromosome statistics
| Name |
Length |
Mapped bases |
Mean coverage |
Standard deviation |
| I |
15072421 |
467401058 |
31.01 |
36.49 |
| II |
15279324 |
456673231 |
29.89 |
9.13 |
| III |
13783682 |
416692735 |
30.23 |
9.81 |
| IV |
17493784 |
545502943 |
31.18 |
10.46 |
| V |
20924143 |
635041765 |
30.35 |
18.85 |
| X |
17718854 |
553489637 |
31.24 |
8.75 |
| MtDNA |
13794 |
19964410 |
1,447.33 |
346.72 |
Input data and parameters
Alignment
| BAM file: |
/home/kokonech/qualimap_release_data/alignments/ERR089819.bam |
| Program: |
Bowtie (0.12.7) |
| Command line: |
"bowtie -S -m 1 -k 1 -p 16 -X 3000 --fr --chunkmbs
2056 /data/scratch/ebwts/c_elegans_ws200 -1 ERR089819_1.fastq -2
ERR089819_2.fastq" |
| Number of windows: |
400 |
| Analysis date: |
Tue Jul 24 12:04:58 CEST 2012 |
| Draw chromosome limits: |
yes
|
Coverage across reference
Coverage Histogram (0-50X)
Duplication Rate Histogram
Mapped Reads Nucleotide Content
Mapped Reads GC-content Distribution
Mapping Quality Across Reference
Mapping Quality Histogram
Insert Size Across Reference
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