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Oryza sativa Japonica Group vs Aegilops tauschii LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Aegilops tauschii (Aegilops tauschii subsp. strangulata, Aet_v4.0) 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.


Number of alignment blocks: 325,785

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

Uncovered: 294,219,203 out of 375,049,285
Covered: 80,830,082 out of 375,049,285

Uncovered: 3,392,938 out of 34,403,043
Matches: 24,079,613 out of 34,403,043
Mismatches: 6,081,485 out of 34,403,043
Insertions: 849,007 out of 34,403,043

Aegilops tauschii subsp. strangulata

Uncovered: 4,094,347,807 out of 4,224,915,394
Covered: 130,567,587 out of 4,224,915,394

Uncovered: 8,062,791 out of 53,210,770
Matches: 34,532,047 out of 53,210,770
Mismatches: 9,366,152 out of 53,210,770
Insertions: 1,249,780 out of 53,210,770

Configuration parameters

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)
     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 Aegilops tauschii
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}