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Medicago truncatula vs Rosa chinensis LastZ results

Medicago truncatula (Medicago truncatula, MtrunA17r5.0_ANR) and Rosa chinensis (Rosa chinensis, RchiOBHm-V2) 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 truncatulaRosa chinensis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 259,676 alignment blocks

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

Uncovered: 373,049,909 out of 429,196,467
Covered: 56,146,558 out of 429,196,467

Uncovered: 13,274,718 out of 45,081,035
Matches: 22,074,105 out of 45,081,035
Mismatches: 9,016,522 out of 45,081,035
Insertions: 715,690 out of 45,081,035
Identity over aligned base-pairs: 69.4%

Rosa chinensis

Uncovered: 443,905,272 out of 515,588,973
Covered: 71,683,701 out of 515,588,973

Uncovered: 11,708,982 out of 43,773,732
Matches: 21,921,655 out of 43,773,732
Mismatches: 9,278,636 out of 43,773,732
Insertions: 864,459 out of 43,773,732
Identity over aligned base-pairs: 68.4%

Block size distribution

Size range All 259,676 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,950
10.1 kb
10 bp - 100 bp
41,672
2.8 Mb
16,433
1.1 Mb
100 bp - 1 kb
195,472
66.0 Mb
77,786
27.1 Mb
1 kb - 10 kb
20,580
32.3 Mb
27,388
62.4 Mb
10 kb - 100 kb
2
33.9 kb
489
9.5 Mb
100 kb - 1 Mb
7
1.1 Mb