Coverage analysis of chromosome contig_2

Coverage

The following figures shows the per-base coverage along the reference genome (black line). The blue line indicates the running median. From the normalised coverage, we estimate z-scores on a per-base level. The red lines indicates the z-scores at plus or minus N standard deviations, where N is chosen by the user. (default:4). Only a million point are shown. This may explain some visual discrepancies with.

Subcoverage

Subchromosome

Basic stats

Here are some basic statistics about the genome coverage.

• BOC (breadth of coverage: the proportion (in %s) of the genome covered by at least one read.): 100.00
• CV (the coefficient of variation.): 0.13
• DOC (the sequencing depth (Depth of Coverage), that is the average the genome coverage.): 49.18
• MAD (median of the absolute median deviation defined as median(|X-median(X)|).): 5.00
• Median (Median of the coverage.): 48.00
• STD (standard deviation.): 6.21
• GC (GC content (%)): 35.15

Regions Of Interest (ROI)

The following tables give regions of interest detected by sequana. Here are the definitions of the columns:

• mean_cov: the average of coverage
• mean_rm: the average of running median
• mean_zscore: the average of zscore
• max_zscore: the higher zscore contains in the region

Low coverage region

Regions with a z-score lower than -2.00 and at least one base with a z-score lower than -4.00 are detected.There are 12 low regions of interest.

chr,start,end,size,mean_cov,max_cov,mean_rm,mean_zscore,max_zscore,log2_ratio,link
contig_2,1697,1698,1,36,36,41,-5.05,-5.05,-0.188,subplots/contig_2_1_12729.html
contig_2,2103,2825,722,38.1,39,41,-2.98,-7.01,-0.106,subplots/contig_2_1_12729.html
contig_2,4354,4355,1,41,41,46,-4.52,-4.52,-0.166,subplots/contig_2_1_12729.html
contig_2,4525,4526,1,41,41,46,-4.52,-4.52,-0.166,subplots/contig_2_1_12729.html
contig_2,5147,5148,1,40,40,47,-6.13,-6.13,-0.233,subplots/contig_2_1_12729.html
contig_2,5934,5935,1,43,43,48,-4.33,-4.33,-0.159,subplots/contig_2_1_12729.html
contig_2,6415,6416,1,44,44,49,-4.25,-4.25,-0.155,subplots/contig_2_1_12729.html
contig_2,6597,6598,1,43,43,49,-5.07,-5.07,-0.188,subplots/contig_2_1_12729.html
contig_2,7434,7435,1,46,46,51,-4.09,-4.09,-0.149,subplots/contig_2_1_12729.html
contig_2,7474,7475,1,41,41,51,-8.03,-8.03,-0.315,subplots/contig_2_1_12729.html
contig_2,8481,8482,1,49,49,56,-5.17,-5.17,-0.193,subplots/contig_2_1_12729.html
contig_2,9425,9426,1,49,49,58,-6.38,-6.38,-0.243,subplots/contig_2_1_12729.html

chr	start	end	size	mean_cov	max_cov	mean_rm	mean_zscore	max_zscore	log2_ratio	link

High coverage region

Regions with a z-score higher than 2.00 and at least one base with a z-score higher than 4.00 are detected.There are 0 high regions of interest.

chr,start,end,size,mean_cov,max_cov,mean_rm,mean_zscore,max_zscore,log2_ratio,link

chr	start	end	size	mean_cov	max_cov	mean_rm	mean_zscore	max_zscore	log2_ratio	link

Coverage histogram

The following figures contain the histogram of the genome coverage. The X and Y axis being in log scale in the left panelwhile only the Y axis is in log scale in the right panel.

Coverage vs GC content

The correlation coefficient between the coverage and GC content is 0.209 with a window size of 201bp.

image not created

Note: the correlation coefficient has to be between -1.0 and 1.0. A coefficient of 0 means no correlation, while a coefficient of -1 or 1 means an existing correlation between GC and Coverage

Normalised coverage

Distribution of the normalised coverage with predicted Gaussian. The red line should be followed the trend of the barplot.

Z-Score distribution

Distribution of the z-score (normalised coverage); You should see a Gaussian distribution centered around 0. The estimated parameters are mu=1.00 and sigma=0.02.

Command

Command used:

sequana_coverage --input-file hifi3/minimap2/hifi3.bed -H 4.0 -L -4.0 --clustering-parameter 0.5 --chunk-size 5000000 --window-gc 201 --mixture-models 2 --output-directory hifi3/sequana_coverage --window-median 20001 --reference-file hifi3/sorted_contigs/hifi3.fasta
Sequana version: 0.18.0

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