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Hordeum vulgare vs Triticum aestivum LastZ results

Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) and Triticum aestivum (Triticum aestivum, IWGSC) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Hordeum vulgare 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)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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

ParameterHordeum vulgareTriticum aestivum
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 6,002,378 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hordeum vulgare

Uncovered: 3,691,532,476 out of 4,833,907,081
Covered: 1,142,374,605 out of 4,833,907,081

Uncovered: 1,616,305 out of 44,392,268
Matches: 38,178,870 out of 44,392,268
Mismatches: 4,004,501 out of 44,392,268
Insertions: 592,592 out of 44,392,268
Identity over aligned base-pairs: 89.3%

Triticum aestivum

Uncovered: 11,452,554,775 out of 14,547,261,565
Covered: 3,094,706,790 out of 14,547,261,565

Uncovered: 5,314,235 out of 136,655,258
Matches: 112,863,839 out of 136,655,258
Mismatches: 17,064,308 out of 136,655,258
Insertions: 1,412,876 out of 136,655,258
Identity over aligned base-pairs: 85.9%

Block size distribution

Size range All 6,002,378 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
82,980
445.1 kb
10 bp - 100 bp
1,130,883
70.5 Mb
496,856
34.0 Mb
100 bp - 1 kb
3,838,843
1.4 Gb
1,974,975
740.0 Mb
1 kb - 10 kb
927,523
1.9 Gb
834,463
2.2 Gb
10 kb - 100 kb
21,886
561.6 Mb
38,703
874.5 Mb
100 kb - 1 Mb
263
29.8 Mb
747
96.0 Mb