Pythium ultimum vs Phytophthora ramorum Translated Blat Results

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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 74. Pythium ultimum was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 65,480

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum DAOM BR144

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

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

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

Pythium ultimum Phytophthora ramorum
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}