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Triticum aestivum vs Secale cereale LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Secale cereale (Secale cereale, Rye_Lo7_2018_v1p1p1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Triticum aestivum 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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

ParameterTriticum aestivumSecale cereale
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 4,875,575 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 12,344,693,678 out of 14,547,261,565
Covered: 2,202,567,887 out of 14,547,261,565

Uncovered: 6,090,989 out of 133,674,966
Matches: 118,633,980 out of 133,674,966
Mismatches: 8,087,971 out of 133,674,966
Insertions: 862,026 out of 133,674,966
Identity over aligned base-pairs: 93.0%

Secale cereale

Uncovered: 5,640,914,224 out of 6,735,227,109
Covered: 1,094,312,885 out of 6,735,227,109

Uncovered: 806,226 out of 44,182,623
Matches: 40,689,829 out of 44,182,623
Mismatches: 2,439,883 out of 44,182,623
Insertions: 246,685 out of 44,182,623
Identity over aligned base-pairs: 93.8%

Block size distribution

Size range All 4,875,575 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
74,017
408.4 kb
10 bp - 100 bp
1,043,887
59.8 Mb
375,826
23.2 Mb
100 bp - 1 kb
2,923,562
1.1 Gb
1,149,635
458.0 Mb
1 kb - 10 kb
832,545
1.7 Gb
626,992
1.7 Gb
10 kb - 100 kb
1,473
36.1 Mb
17,719
302.5 Mb
100 kb - 1 Mb
91
11.5 Mb
616
136.2 Mb
1 Mb - 10 Mb
75
212.8 Mb
10 Mb - 100 Mb
7
104.3 Mb