Phytophthora infestans vs Albugo laibachii Translated Blat results

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 70. Phytophthora infestans was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

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

ParameterPhytophthora infestansAlbugo laibachii
Chunk size1,000,0001,000,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 43,000 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

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
Identity over aligned base-pairs: 66.8%

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
Identity over aligned base-pairs: 67.0%