Brachypodium distachyon vs Oryza sativa Indica LastZ Results

Back to all analyses

Brachypodium distachyon (Brachypodium distachyon, v1.0) and Oryza sativa Indica (Oryza sativa Indica Group, ASM465v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Brachypodium distachyon was used as the reference species. After running LastZ, the raw LastZ 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: 195,051

Genome coverage (bp) Coding exon coverage (bp)
Brachypodium distachyon

Uncovered: 193,561,937 out of 271,923,306
Covered: 78,361,369 out of 271,923,306

Uncovered: 2,638,940 out of 34,177,820
Matches: 24,923,809 out of 34,177,820
Mismatches: 5,902,317 out of 34,177,820
Insertions: 712,754 out of 34,177,820

Oryza sativa Indica Group

Uncovered: 343,353,479 out of 427,004,890
Covered: 83,651,411 out of 427,004,890

Uncovered: 9,026,914 out of 45,465,969
Matches: 28,166,362 out of 45,465,969
Mismatches: 7,275,546 out of 45,465,969
Insertions: 997,147 out of 45,465,969

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Brachypodium distachyon Oryza sativa Indica
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}