Oryza sativa Japonica vs Aegilops tauschii LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Aegilops tauschii (Aegilops tauschii, ASM34733v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. Oryza sativa Japonica 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: 82,921

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

Uncovered: 338,138,881 out of 374,424,240
Covered: 36,285,359 out of 374,424,240

Uncovered: 16,724,635 out of 34,124,807
Matches: 12,457,410 out of 34,124,807
Mismatches: 4,381,956 out of 34,124,807
Insertions: 560,806 out of 34,124,807

Aegilops tauschii

Uncovered: 3,294,646,003 out of 3,313,764,331
Covered: 19,118,328 out of 3,313,764,331

Uncovered: 33,733,279 out of 40,791,602
Matches: 5,393,942 out of 40,791,602
Mismatches: 1,497,228 out of 40,791,602
Insertions: 167,153 out of 40,791,602

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)