Albugo laibachii vs Hyaloperonospora arabidopsidis Translated Blat Results

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Albugo laibachii (Albugo laibachii, ENA1) 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. Albugo laibachii 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: 37,993

Genome coverage (bp) Coding exon coverage (bp)
Albugo laibachii

Uncovered: 26,748,476 out of 32,766,811
Covered: 6,018,335 out of 32,766,811

Uncovered: 11,632,158 out of 15,902,867
Matches: 2,900,337 out of 15,902,867
Mismatches: 1,368,969 out of 15,902,867
Insertions: 1,403 out of 15,902,867

Hyaloperonospora arabidopsidis

Uncovered: 74,716,308 out of 78,897,814
Covered: 4,181,506 out of 78,897,814

Uncovered: 10,021,426 out of 13,171,834
Matches: 2,120,683 out of 13,171,834
Mismatches: 1,029,241 out of 13,171,834
Insertions: 484 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

Albugo laibachii 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}