Phytophthora kernoviae vs Pythium ultimum Translated Blat Results

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Phytophthora kernoviae (Phytophthora kernoviae 00238/432, PhyKer238_432v1) 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. Phytophthora kernoviae 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: 61,250

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora kernoviae 00238/432

Uncovered: 31,551,746 out of 43,208,681
Covered: 11,656,935 out of 43,208,681

Uncovered: 4,718,010 out of 11,508,642
Matches: 4,934,949 out of 11,508,642
Mismatches: 1,852,317 out of 11,508,642
Insertions: 3,366 out of 11,508,642

Pythium ultimum DAOM BR144

Uncovered: 34,513,452 out of 44,913,582
Covered: 10,400,130 out of 44,913,582

Uncovered: 10,707,369 out of 19,826,256
Matches: 6,498,714 out of 19,826,256
Mismatches: 2,616,729 out of 19,826,256
Insertions: 3,444 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

Phytophthora kernoviae 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}