Hyaloperonospora arabidopsidis vs Pythium ultimum Translated Blat Results

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Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Pythium ultimum (Pythium ultimum DAOM BR144, pug) 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: 48,368

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

Uncovered: 70,680,280 out of 78,897,814
Covered: 8,217,534 out of 78,897,814

Uncovered: 7,086,354 out of 13,171,834
Matches: 4,350,868 out of 13,171,834
Mismatches: 1,732,224 out of 13,171,834
Insertions: 2,388 out of 13,171,834

Pythium ultimum DAOM BR144

Uncovered: 38,185,208 out of 44,913,582
Covered: 6,728,374 out of 44,913,582

Uncovered: 13,969,913 out of 19,826,256
Matches: 4,190,164 out of 19,826,256
Mismatches: 1,664,645 out of 19,826,256
Insertions: 1,534 out of 19,826,256

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 Pythium ultimum
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}