Phytophthora parasitica vs Pythium ultimum Translated Blat Results

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Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_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. Phytophthora parasitica 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: 68,113

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora parasitica P1569

Uncovered: 42,304,501 out of 55,229,644
Covered: 12,925,143 out of 55,229,644

Uncovered: 15,776,772 out of 27,601,672
Matches: 8,407,186 out of 27,601,672
Mismatches: 3,412,820 out of 27,601,672
Insertions: 4,894 out of 27,601,672

Pythium ultimum DAOM BR144

Uncovered: 34,270,804 out of 44,913,582
Covered: 10,642,778 out of 44,913,582

Uncovered: 10,546,125 out of 19,826,256
Matches: 6,637,262 out of 19,826,256
Mismatches: 2,638,640 out of 19,826,256
Insertions: 4,229 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

Phytophthora parasitica 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}