Pythium arrhenomanes vs Albugo laibachii Translated Blat results

Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium arrhenomanes was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Minimum score (minScore)30
Database type (t)dnax
Query type (q)dnax
Mask out repeats (mask)lower
Mask out repeats on query (qMask)lower

Chunking parameters

ParameterPythium arrhenomanesAlbugo laibachii
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 26,293 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes

Uncovered: 40,030,973 out of 44,672,625
Covered: 4,641,652 out of 44,672,625

Uncovered: 14,267,055 out of 18,367,184
Matches: 2,729,820 out of 18,367,184
Mismatches: 1,369,742 out of 18,367,184
Insertions: 567 out of 18,367,184
Identity over aligned base-pairs: 66.6%

Albugo laibachii

Uncovered: 28,548,545 out of 32,766,811
Covered: 4,218,266 out of 32,766,811

Uncovered: 11,939,890 out of 15,902,867
Matches: 2,645,353 out of 15,902,867
Mismatches: 1,316,815 out of 15,902,867
Insertions: 809 out of 15,902,867
Identity over aligned base-pairs: 66.8%