Pythium iwayamai vs Pythium ultimum Translated Blat results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) 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 75. Pythium iwayamai 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 iwayamaiPythium 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 82,096 alignment blocks

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

Uncovered: 27,569,150 out of 43,199,174
Covered: 15,630,024 out of 43,199,174

Uncovered: 6,274,778 out of 19,552,457
Matches: 10,270,628 out of 19,552,457
Mismatches: 2,993,840 out of 19,552,457
Insertions: 13,211 out of 19,552,457
Identity over aligned base-pairs: 77.4%

Pythium ultimum

Uncovered: 30,474,389 out of 44,913,582
Covered: 14,439,193 out of 44,913,582

Uncovered: 7,658,508 out of 19,826,256
Matches: 9,471,953 out of 19,826,256
Mismatches: 2,684,741 out of 19,826,256
Insertions: 11,054 out of 19,826,256
Identity over aligned base-pairs: 77.8%