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Medicago truncatula vs Lupinus angustifolius LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Lupinus angustifolius (Lupinus angustifolius, LupAngTanjil_v1.0) 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 truncatulaLupinus angustifolius
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 445,766 alignment blocks

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

Uncovered: 316,466,329 out of 412,800,391
Covered: 96,334,062 out of 412,800,391

Uncovered: 10,881,598 out of 50,132,764
Matches: 29,926,035 out of 50,132,764
Mismatches: 8,461,897 out of 50,132,764
Insertions: 863,234 out of 50,132,764
Identity over aligned base-pairs: 76.2%

Lupinus angustifolius

Uncovered: 464,158,752 out of 609,203,021
Covered: 145,044,269 out of 609,203,021

Uncovered: 2,186,065 out of 42,631,353
Matches: 31,817,994 out of 42,631,353
Mismatches: 7,777,922 out of 42,631,353
Insertions: 849,372 out of 42,631,353
Identity over aligned base-pairs: 78.7%

Block size distribution

Size range All 445,766 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,025
29.7 kb
10 bp - 100 bp
81,617
5.0 Mb
32,896
2.3 Mb
100 bp - 1 kb
315,920
114.7 Mb
124,948
40.6 Mb
1 kb - 10 kb
43,131
71.2 Mb
30,930
77.8 Mb
10 kb - 100 kb
72
1.9 Mb
1,136
24.6 Mb
100 kb - 1 Mb
1
100.0 kb
119
37.1 Mb
1 Mb - 10 Mb
9
10.5 Mb