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Medicago truncatula vs Brassica oleracea LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Brassica oleracea (Brassica oleracea var. oleracea, BOL) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 truncatulaBrassica oleracea
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 243,824 alignment blocks

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

Uncovered: 365,933,168 out of 412,800,391
Covered: 46,867,223 out of 412,800,391

Uncovered: 20,192,858 out of 50,132,764
Matches: 19,670,985 out of 50,132,764
Mismatches: 9,395,116 out of 50,132,764
Insertions: 873,805 out of 50,132,764
Identity over aligned base-pairs: 65.7%

Brassica oleracea

Uncovered: 427,610,131 out of 488,622,507
Covered: 61,012,376 out of 488,622,507

Uncovered: 23,448,172 out of 61,722,508
Matches: 25,572,879 out of 61,722,508
Mismatches: 11,851,443 out of 61,722,508
Insertions: 850,014 out of 61,722,508
Identity over aligned base-pairs: 66.8%

Block size distribution

Size range All 243,824 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,136
11.6 kb
10 bp - 100 bp
39,005
2.6 Mb
10,303
729.2 kb
100 bp - 1 kb
188,944
62.7 Mb
59,048
22.5 Mb
1 kb - 10 kb
13,700
20.4 Mb
28,140
60.8 Mb
10 kb - 100 kb
39
1.3 Mb
161
3.0 Mb