Trypanosoma brucei vs Pythium ultimum Translated Blat Results

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Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) 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. Trypanosoma brucei 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: 3,468

Genome coverage (bp) Coding exon coverage (bp)
Trypanosoma brucei

Uncovered: 25,287,155 out of 25,789,186
Covered: 502,031 out of 25,789,186

Uncovered: 12,677,670 out of 13,171,744
Matches: 319,097 out of 13,171,744
Mismatches: 174,953 out of 13,171,744
Insertions: 24 out of 13,171,744

Pythium ultimum DAOM BR144

Uncovered: 44,503,758 out of 44,913,582
Covered: 409,824 out of 44,913,582

Uncovered: 19,457,312 out of 19,826,256
Matches: 237,506 out of 19,826,256
Mismatches: 131,366 out of 19,826,256
Insertions: 72 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

Trypanosoma brucei 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}