Phaeodactylum tricornutum vs Pythium ultimum Translated Blat Results

Back to all analyses

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) 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. Phaeodactylum tricornutum 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: 6,821

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum CCAP 1055/1

Uncovered: 26,543,060 out of 27,568,093
Covered: 1,025,033 out of 27,568,093

Uncovered: 13,443,278 out of 14,407,044
Matches: 635,242 out of 14,407,044
Mismatches: 328,292 out of 14,407,044
Insertions: 232 out of 14,407,044

Pythium ultimum DAOM BR144

Uncovered: 44,006,317 out of 44,913,582
Covered: 907,265 out of 44,913,582

Uncovered: 18,993,666 out of 19,826,256
Matches: 548,322 out of 19,826,256
Mismatches: 284,133 out of 19,826,256
Insertions: 135 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

Phaeodactylum tricornutum 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}