Pythium ultimum vs Phytophthora ramorum Translated Blat results

Pythium ultimum (Pythium ultimum DAOM BR144, pug) 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 62. Pythium ultimum 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 ultimumPhytophthora 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 65,480 alignment blocks

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

Uncovered: 32,965,547 out of 44,913,582
Covered: 11,948,035 out of 44,913,582

Uncovered: 9,511,332 out of 19,826,256
Matches: 7,451,963 out of 19,826,256
Mismatches: 2,858,018 out of 19,826,256
Insertions: 4,943 out of 19,826,256
Identity over aligned base-pairs: 72.2%

Phytophthora ramorum

Uncovered: 55,998,405 out of 66,652,401
Covered: 10,653,996 out of 66,652,401

Uncovered: 13,336,718 out of 22,377,278
Matches: 6,594,071 out of 22,377,278
Mismatches: 2,442,269 out of 22,377,278
Insertions: 4,220 out of 22,377,278
Identity over aligned base-pairs: 72.9%