Phytophthora lateralis vs Hyaloperonospora arabidopsidis Translated Blat Results

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Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) and Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) 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: 48,852

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

Uncovered: 33,309,500 out of 43,981,379
Covered: 10,671,879 out of 43,981,379

Uncovered: 6,913,432 out of 14,663,433
Matches: 5,875,060 out of 14,663,433
Mismatches: 1,870,165 out of 14,663,433
Insertions: 4,776 out of 14,663,433

Hyaloperonospora arabidopsidis

Uncovered: 70,158,735 out of 78,897,814
Covered: 8,739,079 out of 78,897,814

Uncovered: 6,172,635 out of 13,171,834
Matches: 5,356,138 out of 13,171,834
Mismatches: 1,635,792 out of 13,171,834
Insertions: 7,269 out of 13,171,834

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 Hyaloperonospora arabidopsidis
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}