Effective Genome Size¶
A number of tools can accept an “effective genome size”. This is defined as the length of the “mappable” genome. There are two common alternative ways to calculate this:
1. The number of non-N bases in the genome.
2. The number of regions (of some size) in the genome that are uniquely mappable (possibly given some maximal edit distance).
Option 1 can be computed using faCount from Kent’s tools. The effective genome size for a number of genomes using this method is given below:
Genome |
Effective size |
|---|---|
GRCh37 |
2864785220 |
GRCh38 |
2913022398 |
GRCm37 |
2620345972 |
GRCm38 |
2652783500 |
dm3 |
162367812 |
dm6 |
142573017 |
GRCz10 |
1369631918 |
WBcel235 |
100286401 |
TAIR10 |
119481543 |
These values only appropriate if multimapping reads are included. If they are excluded (or there’s any MAPQ filter applied), then values derived from option 2 are more appropriate. These are then based on the read length. We can approximate these values for various read lengths using the khmer program program and unique-kmers.py in particular. A table of effective genome sizes given a read length using this method is provided below:
Read length |
GRCh37 |
GRCh38 |
GRCm37 |
GRCm38 |
dm3 |
dm6 |
GRCz10 |
WBcel235 |
|---|---|---|---|---|---|---|---|---|
50 |
2685511504 |
2701495761 |
2304947926 |
2308125349 |
130428560 |
125464728 |
1195445591 |
95159452 |
75 |
2736124973 |
2747877777 |
2404646224 |
2407883318 |
135004462 |
127324632 |
1251132686 |
96945445 |
100 |
2776919808 |
2805636331 |
2462481010 |
2467481108 |
139647232 |
129789873 |
1280189044 |
98259998 |
150 |
2827437033 |
2862010578 |
2489384235 |
2494787188 |
144307808 |
129941135 |
1312207169 |
98721253 |
200 |
2855464000 |
2887553303 |
2513019276 |
2520869189 |
148524010 |
132509163 |
1321355241 |
98672758 |