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Medicago truncatula vs Glycine max LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. Medicago truncatula was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Chunking parameters

ParameterMedicago truncatulaGlycine max
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 628,250 alignment blocks

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

Uncovered: 304,332,673 out of 429,196,467
Covered: 124,863,794 out of 429,196,467

Uncovered: 6,118,698 out of 45,081,035
Matches: 30,122,471 out of 45,081,035
Mismatches: 7,956,339 out of 45,081,035
Insertions: 883,527 out of 45,081,035
Identity over aligned base-pairs: 77.3%

Glycine max

Uncovered: 792,666,979 out of 978,491,270
Covered: 185,824,291 out of 978,491,270

Uncovered: 10,203,496 out of 65,618,132
Matches: 43,611,403 out of 65,618,132
Mismatches: 10,615,426 out of 65,618,132
Insertions: 1,187,807 out of 65,618,132
Identity over aligned base-pairs: 78.7%

Block size distribution

Size range All 628,250 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10,148
57.1 kb
10 bp - 100 bp
128,006
7.4 Mb
42,171
3.0 Mb
100 bp - 1 kb
437,706
155.1 Mb
178,717
57.9 Mb
1 kb - 10 kb
52,362
84.0 Mb
32,103
74.7 Mb
10 kb - 100 kb
28
480.1 kb
876
20.0 Mb
100 kb - 1 Mb
118
37.4 Mb
1 Mb - 10 Mb
30
54.1 Mb