Bigelowiella natans vs Phaeodactylum tricornutum Translated Blat Results

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Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 74. Bigelowiella natans 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: 6,334

Genome coverage (bp) Coding exon coverage (bp)
Bigelowiella natans CCMP2755

Uncovered: 93,995,812 out of 94,701,163
Covered: 705,351 out of 94,701,163

Uncovered: 28,137,347 out of 28,817,508
Matches: 450,201 out of 28,817,508
Mismatches: 229,936 out of 28,817,508
Insertions: 24 out of 28,817,508

Phaeodactylum tricornutum CCAP 1055/1

Uncovered: 26,998,505 out of 27,568,093
Covered: 569,588 out of 27,568,093

Uncovered: 13,864,221 out of 14,407,044
Matches: 357,869 out of 14,407,044
Mismatches: 184,903 out of 14,407,044
Insertions: 51 out of 14,407,044

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

Bigelowiella natans Phaeodactylum tricornutum
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}