Pythium vexans vs Pythium ultimum Translated Blat Results

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Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium vexans 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: 62,683

Genome coverage (bp) Coding exon coverage (bp)
Pythium vexans DAOM BR484

Uncovered: 22,389,303 out of 33,844,883
Covered: 11,455,580 out of 33,844,883

Uncovered: 8,560,240 out of 18,608,353
Matches: 7,416,427 out of 18,608,353
Mismatches: 2,626,678 out of 18,608,353
Insertions: 5,008 out of 18,608,353

Pythium ultimum DAOM BR144

Uncovered: 34,374,103 out of 44,913,582
Covered: 10,539,479 out of 44,913,582

Uncovered: 10,556,967 out of 19,826,256
Matches: 6,858,871 out of 19,826,256
Mismatches: 2,405,893 out of 19,826,256
Insertions: 4,525 out of 19,826,256

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 vexans Pythium ultimum
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}