Pythium vexans vs Pythium iwayamai Translated Blat results

Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 vexans 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 vexansPythium iwayamai
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 64,424 alignment blocks

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

Uncovered: 22,856,641 out of 33,844,883
Covered: 10,988,242 out of 33,844,883

Uncovered: 9,002,092 out of 18,608,353
Matches: 7,239,064 out of 18,608,353
Mismatches: 2,361,835 out of 18,608,353
Insertions: 5,362 out of 18,608,353
Identity over aligned base-pairs: 75.4%

Pythium iwayamai

Uncovered: 33,439,226 out of 43,199,174
Covered: 9,759,948 out of 43,199,174

Uncovered: 10,802,563 out of 19,552,457
Matches: 6,611,741 out of 19,552,457
Mismatches: 2,133,888 out of 19,552,457
Insertions: 4,265 out of 19,552,457
Identity over aligned base-pairs: 75.6%