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Medicago truncatula vs Populus trichocarpa LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v4) 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 truncatulaPopulus trichocarpa
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 197,564 alignment blocks

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

Uncovered: 376,126,599 out of 429,196,467
Covered: 53,069,868 out of 429,196,467

Uncovered: 14,609,721 out of 45,081,035
Matches: 21,217,204 out of 45,081,035
Mismatches: 8,595,087 out of 45,081,035
Insertions: 659,023 out of 45,081,035
Identity over aligned base-pairs: 69.6%

Populus trichocarpa

Uncovered: 337,922,981 out of 392,162,179
Covered: 54,239,198 out of 392,162,179

Uncovered: 12,782,496 out of 43,896,102
Matches: 21,839,410 out of 43,896,102
Mismatches: 8,483,391 out of 43,896,102
Insertions: 790,805 out of 43,896,102
Identity over aligned base-pairs: 70.2%

Block size distribution

Size range All 197,564 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,309
11.5 kb
10 bp - 100 bp
28,023
1.8 Mb
6,249
450.4 kb
100 bp - 1 kb
151,224
53.3 Mb
38,298
14.5 Mb
1 kb - 10 kb
16,000
24.5 Mb
19,595
48.0 Mb
10 kb - 100 kb
8
107.3 kb
691
14.5 Mb
100 kb - 1 Mb
15
2.3 Mb