Medicago truncatula vs Glycine max LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Glycine max (Glycine max, Glycine_max_v2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 95. 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 size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 586,842 alignment blocks

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

Uncovered: 297,140,757 out of 412,800,391
Covered: 115,659,634 out of 412,800,391

Uncovered: 9,348,669 out of 50,132,764
Matches: 31,419,696 out of 50,132,764
Mismatches: 8,441,004 out of 50,132,764
Insertions: 923,395 out of 50,132,764
Identity over aligned base-pairs: 77.0%

Glycine max

Uncovered: 780,193,479 out of 978,491,270
Covered: 198,297,791 out of 978,491,270

Uncovered: 5,195,015 out of 65,618,132
Matches: 47,582,341 out of 65,618,132
Mismatches: 11,583,376 out of 65,618,132
Insertions: 1,257,400 out of 65,618,132
Identity over aligned base-pairs: 78.7%

Block size distribution

Size range All 586,842 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
7,670
45.7 kb
10 bp - 100 bp
107,077
6.3 Mb
34,362
2.4 Mb
100 bp - 1 kb
416,802
152.4 Mb
154,216
50.1 Mb
1 kb - 10 kb
55,100
89.9 Mb
29,232
70.6 Mb
10 kb - 100 kb
191
4.1 Mb
1,108
26.0 Mb
100 kb - 1 Mb
2
201.0 kb
122
38.3 Mb
1 Mb - 10 Mb
36
65.5 Mb