Phytophthora infestans vs Pythium ultimum Translated Blat results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 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

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

ParameterPhytophthora infestansPythium ultimum
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 82,786 alignment blocks

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

Uncovered: 214,166,949 out of 228,543,505
Covered: 14,376,556 out of 228,543,505

Uncovered: 11,176,336 out of 22,421,425
Matches: 8,015,383 out of 22,421,425
Mismatches: 3,225,220 out of 22,421,425
Insertions: 4,486 out of 22,421,425
Identity over aligned base-pairs: 71.3%

Pythium ultimum

Uncovered: 34,453,636 out of 44,913,582
Covered: 10,459,946 out of 44,913,582

Uncovered: 10,726,340 out of 19,826,256
Matches: 6,498,844 out of 19,826,256
Mismatches: 2,596,595 out of 19,826,256
Insertions: 4,477 out of 19,826,256
Identity over aligned base-pairs: 71.4%