Pythium arrhenomanes vs Hyaloperonospora arabidopsidis Translated Blat Results

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Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_scaffolds_v1) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium arrhenomanes 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: 35,476

Genome coverage (bp) Coding exon coverage (bp)
Pythium arrhenomanes ATCC 12531

Uncovered: 38,504,243 out of 44,672,625
Covered: 6,168,382 out of 44,672,625

Uncovered: 12,981,173 out of 18,367,184
Matches: 3,804,916 out of 18,367,184
Mismatches: 1,579,378 out of 18,367,184
Insertions: 1,717 out of 18,367,184

Hyaloperonospora arabidopsidis

Uncovered: 73,376,297 out of 78,897,814
Covered: 5,521,517 out of 78,897,814

Uncovered: 8,361,315 out of 13,171,834
Matches: 3,417,292 out of 13,171,834
Mismatches: 1,391,571 out of 13,171,834
Insertions: 1,656 out of 13,171,834

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 arrhenomanes Hyaloperonospora arabidopsidis
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}