Hyaloperonospora arabidopsidis vs Phytophthora ramorum Translated Blat Results

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Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Hyaloperonospora arabidopsidis 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: 56,689

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 66,629,651 out of 78,897,814
Covered: 12,268,163 out of 78,897,814

Uncovered: 4,148,112 out of 13,171,834
Matches: 6,930,083 out of 13,171,834
Mismatches: 2,084,437 out of 13,171,834
Insertions: 9,202 out of 13,171,834

Phytophthora ramorum

Uncovered: 56,482,372 out of 66,652,401
Covered: 10,170,029 out of 66,652,401

Uncovered: 13,656,499 out of 22,377,278
Matches: 6,716,854 out of 22,377,278
Mismatches: 1,997,783 out of 22,377,278
Insertions: 6,142 out of 22,377,278

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

Hyaloperonospora arabidopsidis Phytophthora ramorum
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}