Coverage analysis of chromosome contig_1
Report created with Sequana (v0.18.0)
The genome coverage analysis of the chromosome contig_1.
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.
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.): 0.24
- DOC (the sequencing depth (Depth of Coverage), that is the average the genome coverage.): 65.71
- MAD (median of the absolute median deviation defined as median(|X-median(X)|).): 10.00
- Median (Median of the coverage.): 64.00
- STD (standard deviation.): 15.95
- GC (GC content (%)): 37.65
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 58 low regions of interest.
chr,start,end,size,mean_cov,max_cov,mean_rm,mean_zscore,max_zscore,log2_ratio,link contig_1,162488,165525,3037,50.4,58,66.8,-3.66,-5.53,-0.407,subplots/contig_1_1_200001.html contig_1,194264,194700,436,51.8,53,64,-2.84,-4.87,-0.305,subplots/contig_1_1_200001.html contig_1,219275,222426,3151,46.1,51,63.6,-4.08,-6.24,-0.464,subplots/contig_1_200001_400001.html contig_1,286026,286211,185,50.8,51,69,-3.92,-4.3,-0.442,subplots/contig_1_200001_400001.html contig_1,288186,288187,1,51,51,70,-4.03,-4.03,-0.457,subplots/contig_1_200001_400001.html contig_1,289004,289005,1,46,46,71,-5.22,-5.22,-0.626,subplots/contig_1_200001_400001.html contig_1,334865,335193,328,39.8,41,56,-4.3,-5.29,-0.493,subplots/contig_1_200001_400001.html contig_1,341212,342104,892,35.9,40,56,-5.31,-6.61,-0.641,subplots/contig_1_200001_400001.html contig_1,496662,496663,1,63,63,92,-4.68,-4.68,-0.546,subplots/contig_1_400001_600001.html contig_1,513253,513988,735,73.5,76,89,-2.61,-4.01,-0.277,subplots/contig_1_400001_600001.html contig_1,557720,563903,6183,22.2,31,40,-6.58,-10.3,-0.849,subplots/contig_1_400001_600001.html contig_1,617912,621902,3990,38.1,42,51,-3.76,-5.23,-0.421,subplots/contig_1_600001_800001.html contig_1,680069,680070,1,65,65,91,-4.24,-4.24,-0.485,subplots/contig_1_600001_800001.html contig_1,718928,720118,1190,64.2,68,85,-3.63,-4.88,-0.404,subplots/contig_1_600001_800001.html contig_1,767151,767329,178,40.5,41,55,-3.91,-4.05,-0.44,subplots/contig_1_600001_800001.html contig_1,830855,830856,1,45,45,62,-4.07,-4.07,-0.462,subplots/contig_1_800001_1000001.html contig_1,834937,834949,12,48.8,50,62,-3.18,-5.26,-0.347,subplots/contig_1_800001_1000001.html contig_1,889327,889328,1,37,37,51,-4.08,-4.08,-0.463,subplots/contig_1_800001_1000001.html contig_1,890687,891671,984,39.7,42,51,-3.3,-4.65,-0.362,subplots/contig_1_800001_1000001.html contig_1,892452,892453,1,37,37,51,-4.08,-4.08,-0.463,subplots/contig_1_800001_1000001.html contig_1,893139,893140,1,33,33,51,-5.23,-5.23,-0.628,subplots/contig_1_800001_1000001.html contig_1,910306,910569,263,57.7,58,77,-3.72,-4.43,-0.415,subplots/contig_1_800001_1000001.html contig_1,999325,1000116,791,38.3,41,49,-3.24,-4.54,-0.354,subplots/contig_1_800001_1000001.html contig_1,1000712,1002268,1556,37.2,42,49,-3.58,-4.84,-0.398,subplots/contig_1_1000001_1200001.html contig_1,1028167,1031441,3274,44.7,49,63.4,-4.39,-5.88,-0.505,subplots/contig_1_1000001_1200001.html contig_1,1058763,1058764,1,53,53,73,-4.07,-4.07,-0.462,subplots/contig_1_1000001_1200001.html contig_1,1077175,1077376,201,54.5,56,67.4,-2.84,-4.43,-0.304,subplots/contig_1_1000001_1200001.html contig_1,1177678,1178305,627,53.6,55,66.3,-2.85,-4.94,-0.306,subplots/contig_1_1000001_1200001.html contig_1,1327784,1327785,1,40,40,57,-4.43,-4.43,-0.511,subplots/contig_1_1200001_1400001.html contig_1,1329689,1329690,1,41,41,57,-4.17,-4.17,-0.475,subplots/contig_1_1200001_1400001.html contig_1,1387057,1387058,1,36,36,53,-4.76,-4.76,-0.558,subplots/contig_1_1200001_1400001.html contig_1,1398359,1401714,3355,34.1,37,45,-3.59,-4.94,-0.399,subplots/contig_1_1200001_1400001.html contig_1,1470762,1470763,1,36,36,52,-4.57,-4.57,-0.531,subplots/contig_1_1400001_1600001.html contig_1,1481617,1483671,2054,38.1,40,52.5,-4.07,-5.59,-0.463,subplots/contig_1_1400001_1600001.html contig_1,1567390,1567391,1,32,32,45,-4.29,-4.29,-0.492,subplots/contig_1_1400001_1600001.html contig_1,1569248,1569249,1,33,33,46,-4.2,-4.2,-0.479,subplots/contig_1_1400001_1600001.html contig_1,1588229,1588831,602,36.5,38,46,-3.08,-4.2,-0.334,subplots/contig_1_1400001_1600001.html contig_1,1625297,1625298,1,40,40,55,-4.05,-4.05,-0.459,subplots/contig_1_1600001_1800001.html contig_1,1626490,1626491,1,36,36,53,-4.76,-4.76,-0.558,subplots/contig_1_1600001_1800001.html contig_1,1671929,1675107,3178,39.9,43,53,-3.67,-5.59,-0.409,subplots/contig_1_1600001_1800001.html contig_1,1689714,1689715,1,41,41,59,-4.53,-4.53,-0.525,subplots/contig_1_1600001_1800001.html contig_1,1689763,1689764,1,40,40,59,-4.78,-4.78,-0.561,subplots/contig_1_1600001_1800001.html contig_1,1707339,1707757,418,38.9,41,53.3,-4,-4.76,-0.453,subplots/contig_1_1600001_1800001.html contig_1,1757843,1762538,4695,43,49,58,-3.84,-5.62,-0.431,subplots/contig_1_1600001_1800001.html contig_1,1844741,1844742,1,38,38,56,-4.77,-4.77,-0.559,subplots/contig_1_1800001_2000001.html contig_1,1901216,1901217,1,48,48,67,-4.21,-4.21,-0.481,subplots/contig_1_1800001_2000001.html contig_1,1903392,1903746,354,50.9,52,66.9,-3.56,-4.87,-0.395,subplots/contig_1_1800001_2000001.html contig_1,1934221,1934222,1,36,36,50,-4.16,-4.16,-0.474,subplots/contig_1_1800001_2000001.html contig_1,1954556,1954557,1,31,31,49,-5.44,-5.44,-0.661,subplots/contig_1_1800001_2000001.html contig_1,2006320,2006321,1,43,43,64,-4.87,-4.87,-0.574,subplots/contig_1_2000001_2200001.html contig_1,2028301,2028302,1,38,38,57,-4.94,-4.94,-0.585,subplots/contig_1_2000001_2200001.html contig_1,2030535,2030583,48,45.8,46,57,-2.94,-4.43,-0.317,subplots/contig_1_2000001_2200001.html contig_1,2032030,2032267,237,45.4,46,57,-3.04,-4.94,-0.329,subplots/contig_1_2000001_2200001.html contig_1,2093516,2093517,1,46,46,63,-4.01,-4.01,-0.454,subplots/contig_1_2000001_2200001.html contig_1,2143759,2144317,558,45,47,57,-3.14,-5.2,-0.342,subplots/contig_1_2000001_2200001.html contig_1,2163329,2163330,1,44,44,62,-4.31,-4.31,-0.495,subplots/contig_1_2000001_2200001.html contig_1,2176032,2176271,239,51.8,53,65,-3.03,-4.57,-0.328,subplots/contig_1_2000001_2200001.html contig_1,2177438,2177439,1,47,47,65,-4.11,-4.11,-0.468,subplots/contig_1_2000001_2200001.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 17 high regions of interest.
chr,start,end,size,mean_cov,max_cov,mean_rm,mean_zscore,max_zscore,log2_ratio,link contig_1,480790,480963,173,128,130,100,4.13,4.37,0.36,subplots/contig_1_400001_600001.html contig_1,1013433,1015246,1813,86,91,66,4.41,5.53,0.381,subplots/contig_1_1000001_1200001.html contig_1,1167922,1169982,2060,83.5,88,64,4.44,5.48,0.384,subplots/contig_1_1000001_1200001.html contig_1,1170369,1171840,1471,86.1,90,64.4,4.93,5.94,0.42,subplots/contig_1_1000001_1200001.html contig_1,1522745,1522864,119,56.9,57,44,4.29,4.31,0.372,subplots/contig_1_1400001_1600001.html contig_1,1581436,1582693,1257,61.9,64,47.7,4.35,4.97,0.377,subplots/contig_1_1400001_1600001.html contig_1,1616788,1620446,3658,68.2,72,49,5.72,6.87,0.476,subplots/contig_1_1600001_1800001.html contig_1,1836428,1836714,286,73.8,75,58,3.97,4.27,0.348,subplots/contig_1_1800001_2000001.html contig_1,1837221,1837434,213,74.3,75,58,4.1,4.27,0.358,subplots/contig_1_1800001_2000001.html contig_1,1838252,1839057,805,74.1,75,58,4.05,4.27,0.354,subplots/contig_1_1800001_2000001.html contig_1,1908494,1908513,19,76.9,77,60,4.1,4.13,0.358,subplots/contig_1_1800001_2000001.html contig_1,2060072,2060768,696,82,84,64,4.11,4.56,0.358,subplots/contig_1_2000001_2200001.html contig_1,2061572,2061576,4,82,82,64,4.1,4.1,0.358,subplots/contig_1_2000001_2200001.html contig_1,2061577,2061773,196,82,82,64,4.09,4.1,0.357,subplots/contig_1_2000001_2200001.html contig_1,2184399,2184412,13,77,77,60,4.13,4.13,0.36,subplots/contig_1_2000001_2200001.html contig_1,2184413,2186320,1907,76.5,80,59.2,4.25,5.2,0.369,subplots/contig_1_2000001_2200001.html contig_1,2188006,2188165,159,75.7,77,59,4.14,4.45,0.361,subplots/contig_1_2000001_2200001.html
| 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 -0.114 with a window size of 201bp.
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=0.07.
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.