Bigelowiella natans vs Paramecium tetraurelia Translated Blat Results

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Bigelowiella natans (Bigelowiella natans CCMP2755, Bigna1) and Paramecium tetraurelia (Paramecium tetraurelia, ASM16542v1) 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: 3,685

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

Uncovered: 94,294,657 out of 94,701,163
Covered: 406,506 out of 94,701,163

Uncovered: 28,426,902 out of 28,817,508
Matches: 254,963 out of 28,817,508
Mismatches: 135,580 out of 28,817,508
Insertions: 63 out of 28,817,508

Paramecium tetraurelia

Uncovered: 71,743,363 out of 72,094,543
Covered: 351,180 out of 72,094,543

Uncovered: 53,699,558 out of 54,045,570
Matches: 225,178 out of 54,045,570
Mismatches: 120,610 out of 54,045,570
Insertions: 224 out of 54,045,570

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 Paramecium tetraurelia
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}