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Medicago truncatula vs Rosa chinensis LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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 truncatulaRosa chinensis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 257,625 alignment blocks

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

Uncovered: 355,394,543 out of 412,800,391
Covered: 57,405,848 out of 412,800,391

Uncovered: 14,955,199 out of 50,132,764
Matches: 24,363,447 out of 50,132,764
Mismatches: 10,033,858 out of 50,132,764
Insertions: 780,260 out of 50,132,764
Identity over aligned base-pairs: 69.3%

Rosa chinensis

Uncovered: 445,627,942 out of 515,588,973
Covered: 69,961,031 out of 515,588,973

Uncovered: 10,566,808 out of 43,773,732
Matches: 22,677,931 out of 43,773,732
Mismatches: 9,665,166 out of 43,773,732
Insertions: 863,827 out of 43,773,732
Identity over aligned base-pairs: 68.3%

Block size distribution

Size range All 257,625 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,977
10.3 kb
10 bp - 100 bp
41,329
2.8 Mb
15,228
1.1 Mb
100 bp - 1 kb
195,571
64.9 Mb
76,082
26.2 Mb
1 kb - 10 kb
18,671
29.5 Mb
24,785
57.4 Mb
10 kb - 100 kb
76
2.1 Mb
581
13.0 Mb
100 kb - 1 Mb
1
100.1 kb
11
1.7 Mb