Bigelowiella natans vs Pythium ultimum Translated Blat Results

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Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) 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. 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: 7,956

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

Uncovered: 93,847,736 out of 94,701,163
Covered: 853,427 out of 94,701,163

Uncovered: 27,999,168 out of 28,817,508
Matches: 549,590 out of 28,817,508
Mismatches: 268,663 out of 28,817,508
Insertions: 87 out of 28,817,508

Pythium ultimum DAOM BR144

Uncovered: 44,205,446 out of 44,913,582
Covered: 708,136 out of 44,913,582

Uncovered: 19,180,246 out of 19,826,256
Matches: 432,071 out of 19,826,256
Mismatches: 213,897 out of 19,826,256
Insertions: 42 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

Bigelowiella natans 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}