Phytophthora infestans vs Trypanosoma brucei Translated Blat results

Phytophthora infestans (Phytophthora infestans T30-4, ASM14294v1) and Trypanosoma brucei (Trypanosoma brucei, TryBru_Apr2005_chr11) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64) in Ensembl Protists release 70. Phytophthora infestans was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

ParameterPhytophthora infestansTrypanosoma brucei
Chunk size1,000,0001,000,000
Overlap10,00010,000
Group set size100,000,000100,000,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 5,583 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora infestans

Uncovered: 227,867,084 out of 228,543,505
Covered: 676,421 out of 228,543,505

Uncovered: 21,871,205 out of 22,421,425
Matches: 355,628 out of 22,421,425
Mismatches: 194,469 out of 22,421,425
Insertions: 123 out of 22,421,425
Identity over aligned base-pairs: 64.6%

Trypanosoma brucei

Uncovered: 25,385,688 out of 25,789,186
Covered: 403,498 out of 25,789,186

Uncovered: 12,773,971 out of 13,171,744
Matches: 255,773 out of 13,171,744
Mismatches: 141,939 out of 13,171,744
Insertions: 61 out of 13,171,744
Identity over aligned base-pairs: 64.3%