Medicago truncatula vs Oryza sativa Japonica LastZ Results

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Medicago truncatula (Medicago truncatula str. A17, MedtrA17_4.0) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Medicago truncatula 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: 147,443

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula str. A17

Uncovered: 377,376,360 out of 412,800,391
Covered: 35,424,031 out of 412,800,391

Uncovered: 25,211,565 out of 50,132,764
Matches: 16,070,591 out of 50,132,764
Mismatches: 8,345,660 out of 50,132,764
Insertions: 504,948 out of 50,132,764

Oryza sativa Japonica Group

Uncovered: 343,863,643 out of 374,424,240
Covered: 30,560,597 out of 374,424,240

Uncovered: 16,015,897 out of 34,124,807
Matches: 11,656,146 out of 34,124,807
Mismatches: 6,058,815 out of 34,124,807
Insertions: 393,949 out of 34,124,807

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

Medicago truncatula Oryza sativa Japonica
Chunk size 20,000,000 20,100,000
Overlap 10,000 10,000
Group set size 0 20,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}