Medicago truncatula vs Glycine max LastZ Results

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Medicago truncatula (Medicago truncatula str. A17, MedtrA17_4.0) and Glycine max (Glycine max, V1.0) 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: 671,270

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

Uncovered: 292,659,918 out of 412,800,391
Covered: 120,140,473 out of 412,800,391

Uncovered: 7,776,805 out of 50,132,764
Matches: 32,661,187 out of 50,132,764
Mismatches: 8,723,944 out of 50,132,764
Insertions: 970,828 out of 50,132,764

Glycine max

Uncovered: 744,918,036 out of 973,344,380
Covered: 228,426,344 out of 973,344,380

Uncovered: 3,728,343 out of 64,476,920
Matches: 48,140,034 out of 64,476,920
Mismatches: 11,355,296 out of 64,476,920
Insertions: 1,253,247 out of 64,476,920

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 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}