Phytophthora kernoviae vs Hyaloperonospora arabidopsidis Translated Blat Results

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Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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 kernoviae 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: 45,629

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora kernoviae 00238/432

Uncovered: 32,505,142 out of 43,208,681
Covered: 10,703,539 out of 43,208,681

Uncovered: 4,848,322 out of 11,508,642
Matches: 5,001,757 out of 11,508,642
Mismatches: 1,655,050 out of 11,508,642
Insertions: 3,513 out of 11,508,642

Hyaloperonospora arabidopsidis

Uncovered: 69,561,557 out of 78,897,814
Covered: 9,336,257 out of 78,897,814

Uncovered: 5,179,652 out of 13,171,834
Matches: 5,971,022 out of 13,171,834
Mismatches: 2,015,849 out of 13,171,834
Insertions: 5,311 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 kernoviae 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}