Pythium iwayamai vs Phytophthora ramorum Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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 iwayamaiPhytophthora 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 62,828 alignment blocks

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

Uncovered: 32,346,629 out of 43,199,174
Covered: 10,852,545 out of 43,199,174

Uncovered: 10,032,151 out of 19,552,457
Matches: 6,969,875 out of 19,552,457
Mismatches: 2,546,229 out of 19,552,457
Insertions: 4,202 out of 19,552,457
Identity over aligned base-pairs: 73.2%

Phytophthora ramorum

Uncovered: 56,837,980 out of 66,652,401
Covered: 9,814,421 out of 66,652,401

Uncovered: 14,151,065 out of 22,377,278
Matches: 6,097,985 out of 22,377,278
Mismatches: 2,124,098 out of 22,377,278
Insertions: 4,130 out of 22,377,278
Identity over aligned base-pairs: 74.1%