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Medicago truncatula vs Populus trichocarpa LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v4) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 110. 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 200,292 alignment blocks

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

Uncovered: 358,775,909 out of 412,800,391
Covered: 54,024,482 out of 412,800,391

Uncovered: 17,439,841 out of 50,132,764
Matches: 22,616,015 out of 50,132,764
Mismatches: 9,353,628 out of 50,132,764
Insertions: 723,280 out of 50,132,764
Identity over aligned base-pairs: 69.2%

Populus trichocarpa

Uncovered: 337,657,275 out of 392,162,179
Covered: 54,504,904 out of 392,162,179

Uncovered: 12,594,842 out of 43,896,102
Matches: 21,872,097 out of 43,896,102
Mismatches: 8,638,728 out of 43,896,102
Insertions: 790,435 out of 43,896,102
Identity over aligned base-pairs: 69.9%

Block size distribution

Size range All 200,292 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,330
11.6 kb
10 bp - 100 bp
28,738
1.8 Mb
6,265
450.2 kb
100 bp - 1 kb
153,475
53.6 Mb
38,116
14.2 Mb
1 kb - 10 kb
15,721
24.3 Mb
19,514
47.9 Mb
10 kb - 100 kb
28
796.2 kb
728
15.7 Mb
100 kb - 1 Mb
15
2.2 Mb