Pythium iwayamai vs Pythium ultimum Translated Blat Results

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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 74. Pythium iwayamai was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 82,096

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai DAOM BR242034

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

Pythium ultimum DAOM BR144

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

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

Pythium iwayamai Pythium ultimum
Chunk size 1,000,000 1,000,000
Overlap 10,000 10,000
Group set size 100,000,000 100,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}