Pythium aphanidermatum vs Bigelowiella natans Translated Blat Results

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Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Pythium aphanidermatum 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: 7,392

Genome coverage (bp) Coding exon coverage (bp)
Pythium aphanidermatum DAOM BR444

Uncovered: 35,036,743 out of 35,876,849
Covered: 840,106 out of 35,876,849

Uncovered: 17,232,965 out of 18,015,574
Matches: 521,141 out of 18,015,574
Mismatches: 261,428 out of 18,015,574
Insertions: 40 out of 18,015,574

Bigelowiella natans CCMP2755

Uncovered: 94,018,817 out of 94,701,163
Covered: 682,346 out of 94,701,163

Uncovered: 28,160,140 out of 28,817,508
Matches: 438,024 out of 28,817,508
Mismatches: 219,309 out of 28,817,508
Insertions: 35 out of 28,817,508

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

Pythium aphanidermatum Bigelowiella natans
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}