Medicago truncatula vs Glycine max LastZ Results

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Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . 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: 586,842

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 297,140,757 out of 412,800,391
Covered: 115,659,634 out of 412,800,391

Uncovered: 9,348,669 out of 50,132,764
Matches: 31,419,696 out of 50,132,764
Mismatches: 8,441,004 out of 50,132,764
Insertions: 923,395 out of 50,132,764

Glycine max

Uncovered: 780,193,479 out of 978,491,270
Covered: 198,297,791 out of 978,491,270

Uncovered: 5,195,015 out of 65,618,132
Matches: 47,582,341 out of 65,618,132
Mismatches: 11,583,376 out of 65,618,132
Insertions: 1,257,400 out of 65,618,132

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 Glycine max
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}