11 December 2021, Saturday, 14:38:04
All statistics are based on contigs of size >= 1000 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
Aligned to
"BCep_ref"
|
8605945 bp
|
4 fragments
|
66.61 % G+C
7705 genomic features
Genome statistics | spades_default | spades_kmers_careful | megahit_default | megahit_min_count_3 |
Genome fraction (%) | 98.14 | 98.421 | 98.596 | 98.605 |
Duplication ratio | 1 | 1 | 1.001 | 1.001 |
# genomic features | 7539 + 75 part | 7563 + 62 part | 7540 + 105 part | 7540 + 104 part |
Largest alignment | 455950 | 505898 | 350746 | 350746 |
Total aligned length | 8436553 | 8470789 | 8491768 | 8493173 |
NG50 | 143914 | 217699 | 144335 | 131456 |
NG75 | 79029 | 98944 | 64299 | 62113 |
NA50 | 143914 | 198969 | 144083 | 125159 |
NA75 | 79029 | 103468 | 61973 | 61722 |
NGA50 | 143431 | 198969 | 144083 | 125159 |
NGA75 | 78885 | 98926 | 61722 | 57545 |
LG50 | 17 | 12 | 19 | 20 |
LG75 | 36 | 27 | 41 | 43 |
LA50 | 17 | 13 | 20 | 21 |
LA75 | 37 | 28 | 42 | 44 |
LGA50 | 18 | 13 | 20 | 21 |
LGA75 | 38 | 29 | 43 | 45 |
Reads mapping | ||||
Misassemblies | ||||
# misassemblies | 6 | 6 | 9 | 8 |
# relocations | 6 | 5 | 5 | 4 |
# translocations | 0 | 1 | 4 | 4 |
# inversions | 0 | 0 | 0 | 0 |
# misassembled contigs | 6 | 6 | 9 | 8 |
Misassembled contigs length | 1469048 | 1719134 | 1200775 | 1050989 |
# local misassemblies | 9 | 8 | 4 | 4 |
# scaffold gap ext. mis. | 0 | 0 | 0 | 0 |
# scaffold gap loc. mis. | 0 | 0 | 0 | 0 |
# unaligned mis. contigs | 0 | 0 | 0 | 0 |
Unaligned | ||||
# fully unaligned contigs | 0 | 0 | 0 | 0 |
Fully unaligned length | 0 | 0 | 0 | 0 |
# partially unaligned contigs | 0 | 1 | 0 | 0 |
Partially unaligned length | 0 | 1317 | 0 | 0 |
Mismatches | ||||
# mismatches | 325 | 230 | 208 | 200 |
# indels | 57 | 38 | 26 | 23 |
Indels length | 833 | 466 | 341 | 265 |
# mismatches per 100 kbp | 3.85 | 2.72 | 2.45 | 2.36 |
# indels per 100 kbp | 0.67 | 0.45 | 0.31 | 0.27 |
# indels (<= 5 bp) | 34 | 25 | 19 | 16 |
# indels (> 5 bp) | 23 | 13 | 7 | 7 |
# N's | 0 | 0 | 0 | 0 |
# N's per 100 kbp | 0 | 0 | 0 | 0 |
Statistics without reference | ||||
# contigs | 132 | 91 | 156 | 158 |
# contigs (>= 0 bp) | 288 | 239 | 200 | 198 |
# contigs (>= 1000 bp) | 132 | 91 | 156 | 158 |
# contigs (>= 5000 bp) | 94 | 74 | 118 | 121 |
# contigs (>= 10000 bp) | 87 | 67 | 104 | 108 |
# contigs (>= 25000 bp) | 67 | 58 | 72 | 75 |
# contigs (>= 50000 bp) | 51 | 43 | 49 | 51 |
Largest contig | 754490 | 961949 | 539126 | 539126 |
Total length | 8447218 | 8472540 | 8492269 | 8493797 |
Total length (>= 0 bp) | 8490011 | 8510655 | 8511587 | 8511217 |
Total length (>= 1000 bp) | 8447218 | 8472540 | 8492269 | 8493797 |
Total length (>= 5000 bp) | 8371775 | 8438829 | 8405876 | 8408960 |
Total length (>= 10000 bp) | 8324069 | 8384754 | 8296157 | 8308919 |
Total length (>= 25000 bp) | 8010950 | 8245120 | 7760455 | 7762256 |
Total length (>= 50000 bp) | 7438644 | 7723080 | 6917716 | 6910273 |
N50 | 151907 | 217699 | 144335 | 131456 |
N75 | 85907 | 107910 | 66469 | 64244 |
L50 | 16 | 12 | 19 | 20 |
L75 | 35 | 26 | 40 | 42 |
GC (%) | 66.67 | 66.67 | 66.66 | 66.66 |
K-mer-based statistics | ||||
Predicted genes | ||||
Similarity statistics | ||||
# similar correct contigs | 42 | 25 | 41 | 40 |
# similar misassembled blocks | 7 | 8 | 9 | 8 |
Plots:Cumulative lengthNxNAxNGxNGAxMisassembliesGenomic featuresGC content
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0 20 40 60 80 100 120 140th contig 0 1 2 3 4 5 6 7 8 9 Mbp |
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Contigs are ordered from largest (contig #1) to smallest. |
- Two or more distinct alignments cover the breakpoint.
- The gap between left and right flanking sequences is less than the misassembly threshold (1 kbp by default).
- The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.
- There are two misassembly breakpoints of the same type around a short alignment (less than 7 kbp by default)
- The gap between two long flanking sequences on the sides of the short alignment is less than 7 kbp.
- The long flanking sequences both are on the same strand of the same chromosome of the reference genome.