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Medicago truncatula vs Malus domestica Golden LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Malus domestica Golden (Malus domestica, ASM211411v1) 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 truncatulaMalus domestica Golden
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 258,418 alignment blocks

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

Uncovered: 372,824,584 out of 429,196,467
Covered: 56,371,883 out of 429,196,467

Uncovered: 13,945,001 out of 45,081,035
Matches: 21,554,226 out of 45,081,035
Mismatches: 8,905,714 out of 45,081,035
Insertions: 676,094 out of 45,081,035
Identity over aligned base-pairs: 69.2%

Malus domestica Golden

Uncovered: 634,174,786 out of 702,961,352
Covered: 68,786,566 out of 702,961,352

Uncovered: 12,590,280 out of 47,560,911
Matches: 24,504,862 out of 47,560,911
Mismatches: 9,577,053 out of 47,560,911
Insertions: 888,716 out of 47,560,911
Identity over aligned base-pairs: 70.1%

Block size distribution

Size range All 258,418 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,668
13.7 kb
10 bp - 100 bp
41,645
2.7 Mb
12,427
898.4 kb
100 bp - 1 kb
196,600
65.6 Mb
63,755
21.9 Mb
1 kb - 10 kb
17,433
26.8 Mb
23,032
55.8 Mb
10 kb - 100 kb
72
1.6 Mb
816
16.5 Mb
100 kb - 1 Mb
10
1.7 Mb