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Medicago truncatula vs Quercus lobata LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Quercus lobata (Quercus lobata, ValleyOak3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 107. 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 truncatulaQuercus lobata
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 233,560 alignment blocks

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

Uncovered: 353,659,002 out of 412,800,391
Covered: 59,141,389 out of 412,800,391

Uncovered: 15,384,273 out of 50,132,764
Matches: 24,501,737 out of 50,132,764
Mismatches: 9,515,733 out of 50,132,764
Insertions: 731,021 out of 50,132,764
Identity over aligned base-pairs: 70.5%

Quercus lobata

Uncovered: 780,885,227 out of 846,677,899
Covered: 65,792,672 out of 846,677,899

Uncovered: 19,144,908 out of 49,763,784
Matches: 21,527,846 out of 49,763,784
Mismatches: 8,319,511 out of 49,763,784
Insertions: 771,519 out of 49,763,784
Identity over aligned base-pairs: 70.3%

Block size distribution

Size range All 233,560 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,949
10.5 kb
10 bp - 100 bp
31,764
2.1 Mb
10,745
783.6 kb
100 bp - 1 kb
181,788
62.7 Mb
62,619
22.2 Mb
1 kb - 10 kb
17,993
28.2 Mb
25,183
60.0 Mb
10 kb - 100 kb
65
1.7 Mb
631
11.4 Mb
100 kb - 1 Mb
1
100.1 kb
4
477.2 kb