ABySS 2.2.3 Bloom filter false positive rate

[Peiwen Li]

Hi ABySS group!

I ran abyss-pe with Bloom filter which reported a false positive rate (FPR) in the log file. Below is part of the log file:

....

Loaded 478640000 reads into Bloom filter

Loaded 478650000 reads into Bloom filter

Loaded 478658235 reads from `/home/peiwen/WGS_whitefish_2018/WF_1181_S2_L004_R2_001.fastq.gz` into Bloom filter

Bloom filter FPR: 3.94%

Counting Bloom filter stats:

#counters               = 190887435392

#size (B)               = 190887435392

threshold               = 2

popcount                = 13530549696

FPR                     = 0.00252%

 ....

I wonder which FPR is the one I should keep track of and how the two FPR are different?

Thank you!

Peiwen 

[Johnathan Wong]

For posterity:
Answered in https://github.com/bcgsc/abyss/issues/311