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Medicago truncatula vs Glycine soja (Wild soybean) LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Glycine soja (Wild soybean) (Glycine soja, ASM419377v2) 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 truncatulaGlycine soja (Wild soybean)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 514,897 alignment blocks

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

Uncovered: 317,784,444 out of 429,196,467
Covered: 111,412,023 out of 429,196,467

Uncovered: 6,769,350 out of 45,081,035
Matches: 29,736,290 out of 45,081,035
Mismatches: 7,706,760 out of 45,081,035
Insertions: 868,635 out of 45,081,035
Identity over aligned base-pairs: 77.6%

Glycine soja (Wild soybean)

Uncovered: 847,978,721 out of 1,013,766,566
Covered: 165,787,845 out of 1,013,766,566

Uncovered: 12,407,507 out of 61,659,035
Matches: 39,130,214 out of 61,659,035
Mismatches: 9,098,383 out of 61,659,035
Insertions: 1,022,931 out of 61,659,035
Identity over aligned base-pairs: 79.4%

Block size distribution

Size range All 514,897 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9,855
55.9 kb
10 bp - 100 bp
102,939
5.7 Mb
22,084
1.6 Mb
100 bp - 1 kb
353,997
131.6 Mb
110,878
38.2 Mb
1 kb - 10 kb
48,086
76.8 Mb
26,891
63.9 Mb
10 kb - 100 kb
20
369.2 kb
827
19.2 Mb
100 kb - 1 Mb
118
36.6 Mb
1 Mb - 10 Mb
31
55.2 Mb