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Medicago truncatula vs Glycine soja (Wild soybean) LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Glycine soja (Wild soybean) (Glycine soja, ASM419377v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 111. 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 510,153 alignment blocks

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

Uncovered: 304,162,178 out of 412,800,391
Covered: 108,638,213 out of 412,800,391

Uncovered: 9,755,568 out of 50,132,764
Matches: 31,198,151 out of 50,132,764
Mismatches: 8,263,142 out of 50,132,764
Insertions: 915,903 out of 50,132,764
Identity over aligned base-pairs: 77.3%

Glycine soja (Wild soybean)

Uncovered: 844,866,205 out of 1,013,766,566
Covered: 168,900,361 out of 1,013,766,566

Uncovered: 12,020,056 out of 61,659,035
Matches: 39,328,227 out of 61,659,035
Mismatches: 9,297,621 out of 61,659,035
Insertions: 1,013,131 out of 61,659,035
Identity over aligned base-pairs: 79.2%

Block size distribution

Size range All 510,153 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
9,928
56.1 kb
10 bp - 100 bp
103,191
5.7 Mb
21,241
1.5 Mb
100 bp - 1 kb
350,060
129.8 Mb
105,822
36.5 Mb
1 kb - 10 kb
46,848
75.5 Mb
25,493
61.9 Mb
10 kb - 100 kb
124
3.1 Mb
952
22.8 Mb
100 kb - 1 Mb
2
238.7 kb
121
36.9 Mb
1 Mb - 10 Mb
31
54.9 Mb