Medicago truncatula vs Populus trichocarpa LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 233,016 alignment blocks

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

Uncovered: 352,642,519 out of 412,800,391
Covered: 60,157,872 out of 412,800,391

Uncovered: 14,900,069 out of 50,132,764
Matches: 24,259,681 out of 50,132,764
Mismatches: 10,200,785 out of 50,132,764
Insertions: 772,229 out of 50,132,764
Identity over aligned base-pairs: 68.9%

Populus trichocarpa

Uncovered: 365,994,379 out of 434,132,815
Covered: 68,138,436 out of 434,132,815

Uncovered: 8,583,899 out of 48,383,886
Matches: 27,539,839 out of 48,383,886
Mismatches: 11,241,713 out of 48,383,886
Insertions: 1,018,435 out of 48,383,886
Identity over aligned base-pairs: 69.2%

Block size distribution

Size range All 233,016 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,203
11.4 kb
10 bp - 100 bp
32,814
2.1 Mb
8,405
592.7 kb
100 bp - 1 kb
177,913
62.8 Mb
45,600
16.7 Mb
1 kb - 10 kb
19,979
32.1 Mb
22,902
56.9 Mb
10 kb - 100 kb
107
2.1 Mb
940
20.3 Mb
100 kb - 1 Mb
28
4.5 Mb