Zea mays vs Oryza sativa Japonica LastZ Results

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Zea mays (Zea mays, AGPv4) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 81. Zea mays 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: 224,244

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,032,241,522 out of 2,134,373,047
Covered: 102,131,525 out of 2,134,373,047

Uncovered: 6,106,008 out of 48,311,124
Matches: 32,968,756 out of 48,311,124
Mismatches: 8,212,282 out of 48,311,124
Insertions: 1,024,078 out of 48,311,124

Oryza sativa Japonica Group

Uncovered: 320,757,170 out of 374,424,240
Covered: 53,667,070 out of 374,424,240

Uncovered: 10,628,554 out of 34,124,807
Matches: 18,546,551 out of 34,124,807
Mismatches: 4,370,925 out of 34,124,807
Insertions: 578,777 out of 34,124,807

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Zea mays Oryza sativa Japonica
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}