Paramecium tetraurelia vs Phytophthora infestans Translated Blat Results

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Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) 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 74. Paramecium tetraurelia 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: 8,527

Genome coverage (bp) Coding exon coverage (bp)
Paramecium tetraurelia

Uncovered: 70,837,872 out of 72,094,543
Covered: 1,256,671 out of 72,094,543

Uncovered: 52,817,351 out of 54,045,570
Matches: 765,909 out of 54,045,570
Mismatches: 461,670 out of 54,045,570
Insertions: 640 out of 54,045,570

Phytophthora infestans T30-4

Uncovered: 228,053,968 out of 228,543,505
Covered: 489,537 out of 228,543,505

Uncovered: 21,949,015 out of 22,421,425
Matches: 290,690 out of 22,421,425
Mismatches: 181,669 out of 22,421,425
Insertions: 51 out of 22,421,425

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

Paramecium tetraurelia Phytophthora infestans
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}