Albugo laibachii vs Phytophthora ramorum Translated Blat results

Albugo laibachii (Albugo laibachii, ENA1) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 67. Albugo laibachii 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

ParameterAlbugo laibachiiPhytophthora ramorum
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 31,636 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 27,189,926 out of 32,766,811
Covered: 5,576,885 out of 32,766,811

Uncovered: 11,055,209 out of 15,902,867
Matches: 3,234,649 out of 15,902,867
Mismatches: 1,612,055 out of 15,902,867
Insertions: 954 out of 15,902,867
Identity over aligned base-pairs: 66.7%

Phytophthora ramorum

Uncovered: 62,232,990 out of 66,652,401
Covered: 4,419,411 out of 66,652,401

Uncovered: 18,367,315 out of 22,377,278
Matches: 2,680,235 out of 22,377,278
Mismatches: 1,329,124 out of 22,377,278
Insertions: 604 out of 22,377,278
Identity over aligned base-pairs: 66.8%