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Medicago truncatula vs Quercus lobata LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Quercus lobata (Quercus lobata, ValleyOak3.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 112. 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 238,228 alignment blocks

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

Uncovered: 371,129,234 out of 429,196,467
Covered: 58,067,233 out of 429,196,467

Uncovered: 12,996,520 out of 45,081,035
Matches: 22,732,577 out of 45,081,035
Mismatches: 8,685,428 out of 45,081,035
Insertions: 666,510 out of 45,081,035
Identity over aligned base-pairs: 70.9%

Quercus lobata

Uncovered: 778,384,305 out of 846,677,899
Covered: 68,293,594 out of 846,677,899

Uncovered: 19,664,831 out of 49,763,784
Matches: 21,180,217 out of 49,763,784
Mismatches: 8,140,906 out of 49,763,784
Insertions: 777,830 out of 49,763,784
Identity over aligned base-pairs: 70.4%

Block size distribution

Size range All 238,228 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,994
10.7 kb
10 bp - 100 bp
32,803
2.1 Mb
12,021
866.8 kb
100 bp - 1 kb
183,586
64.0 Mb
65,756
23.5 Mb
1 kb - 10 kb
19,843
31.0 Mb
27,031
63.7 Mb
10 kb - 100 kb
2
38.5 kb
542
9.1 Mb
100 kb - 1 Mb
1
119.4 kb