Guillardia theta CCMP2712 vs Phytophthora infestans Translated Blat results

Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) and Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) 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 CCMP2712Phytophthora infestans
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 9,185 alignment blocks

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

Uncovered: 86,176,941 out of 87,266,873
Covered: 1,089,932 out of 87,266,873

Uncovered: 29,606,635 out of 30,644,092
Matches: 697,658 out of 30,644,092
Mismatches: 339,018 out of 30,644,092
Insertions: 781 out of 30,644,092
Identity over aligned base-pairs: 67.2%

Phytophthora infestans

Uncovered: 227,699,954 out of 228,543,505
Covered: 843,551 out of 228,543,505

Uncovered: 21,612,739 out of 22,421,425
Matches: 543,041 out of 22,421,425
Mismatches: 265,442 out of 22,421,425
Insertions: 203 out of 22,421,425
Identity over aligned base-pairs: 67.2%