Pythium aphanidermatum vs Hyaloperonospora arabidopsidis Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum 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: 34,330

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 29,381,130 out of 35,876,849
Covered: 6,495,719 out of 35,876,849

Uncovered: 12,212,884 out of 18,015,574
Matches: 4,073,004 out of 18,015,574
Mismatches: 1,728,267 out of 18,015,574
Insertions: 1,419 out of 18,015,574

Hyaloperonospora arabidopsidis

Uncovered: 73,151,384 out of 78,897,814
Covered: 5,746,430 out of 78,897,814

Uncovered: 8,141,766 out of 13,171,834
Matches: 3,544,260 out of 13,171,834
Mismatches: 1,483,853 out of 13,171,834
Insertions: 1,955 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 aphanidermatum 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}