Pythium iwayamai vs Bigelowiella natans Translated Blat Results

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Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_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 iwayamai 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: 6,897

Genome coverage (bp) Coding exon coverage (bp)
Pythium iwayamai DAOM BR242034

Uncovered: 42,434,453 out of 43,199,174
Covered: 764,721 out of 43,199,174

Uncovered: 18,854,255 out of 19,552,457
Matches: 469,092 out of 19,552,457
Mismatches: 228,990 out of 19,552,457
Insertions: 120 out of 19,552,457

Bigelowiella natans CCMP2755

Uncovered: 94,077,019 out of 94,701,163
Covered: 624,144 out of 94,701,163

Uncovered: 28,215,688 out of 28,817,508
Matches: 404,190 out of 28,817,508
Mismatches: 197,597 out of 28,817,508
Insertions: 33 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 iwayamai 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}