Phytophthora infestans vs Albugo laibachii Translated Blat Results

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Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Albugo laibachii (Albugo laibachii, ENA1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Phytophthora infestans 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: 43,000

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans T30-4

Uncovered: 221,533,189 out of 228,543,505
Covered: 7,010,316 out of 228,543,505

Uncovered: 17,217,323 out of 22,421,425
Matches: 3,474,800 out of 22,421,425
Mismatches: 1,728,609 out of 22,421,425
Insertions: 693 out of 22,421,425

Albugo laibachii

Uncovered: 28,206,256 out of 32,766,811
Covered: 4,560,555 out of 32,766,811

Uncovered: 11,704,953 out of 15,902,867
Matches: 2,813,608 out of 15,902,867
Mismatches: 1,383,105 out of 15,902,867
Insertions: 1,201 out of 15,902,867

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

Phytophthora infestans Albugo laibachii
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}