Oryza sativa Japonica Group vs Manihot esculenta LastZ results
Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Manihot esculenta (Manihot esculenta, Manihot_esculenta_v6) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. Oryza sativa Japonica Group 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
Parameter | Value |
---|---|
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
Parameter | Oryza sativa Japonica Group | Manihot esculenta |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options | {default_soft_masking => 1} | {default_soft_masking => 1} |
Statistics over 158,027 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Oryza sativa Japonica Group |
Uncovered: 340,030,252 out of 375,049,285 |
Uncovered: 13,951,359 out of 34,403,043 |
Manihot esculenta |
Uncovered: 543,687,258 out of 582,117,524 |
Uncovered: 13,440,730 out of 38,679,430 |
Block size distribution
Size range | All 158,027 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,183 |
5.7 kb |
|||
10 bp - 100 bp | 24,543 |
1.7 Mb |
5,205 |
373.1 kb |
|
100 bp - 1 kb | 123,085 |
39.9 Mb |
33,546 |
13.6 Mb |
|
1 kb - 10 kb | 9,198 |
14.2 Mb |
19,507 |
41.3 Mb |
|
10 kb - 100 kb | 18 |
189.0 kb |
65 |
821.7 kb |