Pythium irregulare vs Phytophthora infestans Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 75. Pythium irregulare 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

ParameterPythium irregularePhytophthora infestans
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 59,557 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium irregulare

Uncovered: 32,061,539 out of 42,968,084
Covered: 10,906,545 out of 42,968,084

Uncovered: 10,723,511 out of 20,543,058
Matches: 7,042,238 out of 20,543,058
Mismatches: 2,772,231 out of 20,543,058
Insertions: 5,078 out of 20,543,058
Identity over aligned base-pairs: 71.7%

Phytophthora infestans

Uncovered: 218,544,852 out of 228,543,505
Covered: 9,998,653 out of 228,543,505

Uncovered: 13,248,934 out of 22,421,425
Matches: 6,608,145 out of 22,421,425
Mismatches: 2,560,304 out of 22,421,425
Insertions: 4,042 out of 22,421,425
Identity over aligned base-pairs: 72.0%