Guillardia theta CCMP2712 vs Pythium iwayamai Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) 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 76. Guillardia theta CCMP2712 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

ParameterGuillardia theta CCMP2712Pythium 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 9,684 alignment blocks

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

Uncovered: 86,192,142 out of 87,266,873
Covered: 1,074,731 out of 87,266,873

Uncovered: 29,619,340 out of 30,644,092
Matches: 703,121 out of 30,644,092
Mismatches: 320,890 out of 30,644,092
Insertions: 741 out of 30,644,092
Identity over aligned base-pairs: 68.6%

Pythium iwayamai

Uncovered: 42,400,714 out of 43,199,174
Covered: 798,460 out of 43,199,174

Uncovered: 18,815,622 out of 19,552,457
Matches: 504,047 out of 19,552,457
Mismatches: 232,612 out of 19,552,457
Insertions: 176 out of 19,552,457
Identity over aligned base-pairs: 68.4%