Pythium aphanidermatum vs Pythium ultimum Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum 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: 57,977

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 24,920,668 out of 35,876,849
Covered: 10,956,181 out of 35,876,849

Uncovered: 8,472,711 out of 18,015,574
Matches: 6,888,341 out of 18,015,574
Mismatches: 2,650,899 out of 18,015,574
Insertions: 3,623 out of 18,015,574

Pythium ultimum DAOM BR144

Uncovered: 34,736,050 out of 44,913,582
Covered: 10,177,532 out of 44,913,582

Uncovered: 10,843,115 out of 19,826,256
Matches: 6,485,807 out of 19,826,256
Mismatches: 2,493,372 out of 19,826,256
Insertions: 3,962 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 aphanidermatum 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}