Oryza sativa Japonica vs Nicotiana attenuata str. UT LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Nicotiana attenuata str. UT (Nicotiana attenuata str. UT, NIATTr2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 119,388

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

Uncovered: 349,211,865 out of 375,049,285
Covered: 25,837,420 out of 375,049,285

Uncovered: 18,279,452 out of 34,403,043
Matches: 10,328,646 out of 34,403,043
Mismatches: 5,450,450 out of 34,403,043
Insertions: 344,495 out of 34,403,043

Nicotiana attenuata str. UT

Uncovered: 1,468,768,444 out of 1,492,146,380
Covered: 23,377,936 out of 1,492,146,380

Uncovered: 9,720,222 out of 23,314,391
Matches: 8,849,754 out of 23,314,391
Mismatches: 4,489,901 out of 23,314,391
Insertions: 254,514 out of 23,314,391

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 Nicotiana attenuata str. UT
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}