Pythium irregulare vs Pythium aphanidermatum Translated Blat results

Pythium irregulare (Pythium irregulare DAOM BR486, pir_scaffolds_v1) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) 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 irregularePythium aphanidermatum
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 59,798 alignment blocks

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

Uncovered: 31,986,506 out of 42,968,084
Covered: 10,981,578 out of 42,968,084

Uncovered: 10,659,661 out of 20,543,058
Matches: 7,164,999 out of 20,543,058
Mismatches: 2,713,208 out of 20,543,058
Insertions: 5,190 out of 20,543,058
Identity over aligned base-pairs: 72.5%

Pythium aphanidermatum

Uncovered: 25,858,494 out of 35,876,849
Covered: 10,018,355 out of 35,876,849

Uncovered: 9,185,962 out of 18,015,574
Matches: 6,434,769 out of 18,015,574
Mismatches: 2,391,040 out of 18,015,574
Insertions: 3,803 out of 18,015,574
Identity over aligned base-pairs: 72.9%