Oryza sativa Japonica Group vs Glycine max LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Glycine max (Glycine max, Glycine_max_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 260,441

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 339,434,153 out of 375,049,285
Covered: 35,615,132 out of 375,049,285

Uncovered: 13,541,366 out of 34,403,043
Matches: 13,439,137 out of 34,403,043
Mismatches: 6,848,347 out of 34,403,043
Insertions: 574,193 out of 34,403,043

Glycine max

Uncovered: 913,056,034 out of 978,416,860
Covered: 65,360,826 out of 978,416,860

Uncovered: 24,595,432 out of 65,631,894
Matches: 27,002,931 out of 65,631,894
Mismatches: 13,170,893 out of 65,631,894
Insertions: 862,638 out of 65,631,894

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

Oryza sativa Japonica Group Glycine max
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}