Guillardia theta CCMP2712 vs Pythium ultimum Translated Blat Results

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Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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. Guillardia theta CCMP2712 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: 9,596

Genome coverage (bp) Coding exon coverage (bp)
Guillardia theta CCMP2712

Uncovered: 86,156,353 out of 87,266,873
Covered: 1,110,520 out of 87,266,873

Uncovered: 29,586,345 out of 30,644,092
Matches: 715,607 out of 30,644,092
Mismatches: 341,196 out of 30,644,092
Insertions: 944 out of 30,644,092

Pythium ultimum DAOM BR144

Uncovered: 44,058,332 out of 44,913,582
Covered: 855,250 out of 44,913,582

Uncovered: 19,045,966 out of 19,826,256
Matches: 526,714 out of 19,826,256
Mismatches: 253,422 out of 19,826,256
Insertions: 154 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

Guillardia theta CCMP2712 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}