Phytophthora lateralis vs Pythium ultimum Translated Blat Results

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Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) 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 lateralis 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: 56,440

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora lateralis MPF4

Uncovered: 33,630,139 out of 43,981,379
Covered: 10,351,240 out of 43,981,379

Uncovered: 7,130,143 out of 14,663,433
Matches: 5,487,134 out of 14,663,433
Mismatches: 2,043,002 out of 14,663,433
Insertions: 3,154 out of 14,663,433

Pythium ultimum DAOM BR144

Uncovered: 36,085,512 out of 44,913,582
Covered: 8,828,070 out of 44,913,582

Uncovered: 12,202,077 out of 19,826,256
Matches: 5,511,847 out of 19,826,256
Mismatches: 2,108,247 out of 19,826,256
Insertions: 4,085 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 lateralis 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}