Pythium vexans vs Pythium aphanidermatum Translated Blat Results

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Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) 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: 55,071

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

Uncovered: 23,954,985 out of 33,844,883
Covered: 9,889,898 out of 33,844,883

Uncovered: 9,848,974 out of 18,608,353
Matches: 6,310,036 out of 18,608,353
Mismatches: 2,445,344 out of 18,608,353
Insertions: 3,999 out of 18,608,353

Pythium aphanidermatum DAOM BR444

Uncovered: 26,963,699 out of 35,876,849
Covered: 8,913,150 out of 35,876,849

Uncovered: 10,101,421 out of 18,015,574
Matches: 5,727,574 out of 18,015,574
Mismatches: 2,183,614 out of 18,015,574
Insertions: 2,965 out of 18,015,574

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 aphanidermatum
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}