Pythium irregulare vs Hyaloperonospora arabidopsidis Translated Blat Results

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Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) 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. Pythium irregulare 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: 39,966

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare DAOM BR486

Uncovered: 35,595,290 out of 42,968,084
Covered: 7,372,794 out of 42,968,084

Uncovered: 13,858,744 out of 20,543,058
Matches: 4,772,633 out of 20,543,058
Mismatches: 1,909,303 out of 20,543,058
Insertions: 2,378 out of 20,543,058

Hyaloperonospora arabidopsidis

Uncovered: 72,390,566 out of 78,897,814
Covered: 6,507,248 out of 78,897,814

Uncovered: 7,532,050 out of 13,171,834
Matches: 4,050,291 out of 13,171,834
Mismatches: 1,587,351 out of 13,171,834
Insertions: 2,142 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

Pythium irregulare 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}