Pythium vexans vs Phytophthora ramorum Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) 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 75. Pythium vexans 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

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 vexansPhytophthora ramorum
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 64,131 alignment blocks

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

Uncovered: 21,918,276 out of 33,844,883
Covered: 11,926,607 out of 33,844,883

Uncovered: 8,188,904 out of 18,608,353
Matches: 7,681,116 out of 18,608,353
Mismatches: 2,732,510 out of 18,608,353
Insertions: 5,823 out of 18,608,353
Identity over aligned base-pairs: 73.7%

Phytophthora ramorum

Uncovered: 55,639,360 out of 66,652,401
Covered: 11,013,041 out of 66,652,401

Uncovered: 12,937,223 out of 22,377,278
Matches: 7,027,243 out of 22,377,278
Mismatches: 2,407,012 out of 22,377,278
Insertions: 5,800 out of 22,377,278
Identity over aligned base-pairs: 74.4%