04 April 2018, Wednesday, 03:29:35
All statistics are based on contigs of size >= 3000 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).
Aligned to "hg38" | 3088286401 bp | 25 fragments | 40.87 % G+C
Genome statistics | UpperBound | Canu | Flye | MaSuRCA |
Genome fraction (%) | 99.074 | 92.249 | 91.909 | 93.707 |
Duplication ratio | 1.002 | 0.998 | 0.99 | 1.018 |
Largest alignment | 75724015 | 25750637 | 21734865 | 22412626 |
Total aligned length | 2916136310 | 2703373535 | 2672642008 | 2799134474 |
NG50 | 7862149 | 3241232 | 3767461 | 4968454 |
NG75 | 3530087 | 1036013 | 1439662 | 2036226 |
NA50 | 8389762 | 3144867 | 3610146 | 4214832 |
NA75 | 3936041 | 1408424 | 1618830 | 2064920 |
NGA50 | 7862149 | 2744681 | 3172168 | 3931830 |
NGA75 | 3530087 | 776072 | 1042595 | 1547559 |
LG50 | 105 | 244 | 227 | 182 |
LG75 | 252 | 649 | 550 | 419 |
LA50 | 95 | 241 | 223 | 201 |
LA75 | 218 | 567 | 510 | 439 |
LGA50 | 105 | 296 | 266 | 226 |
LGA75 | 252 | 795 | 672 | 525 |
Complete BUSCO (%) | 90.1 | 86.47 | 51.49 | 83.5 |
Partial BUSCO (%) | 2.64 | 5.61 | 18.15 | 4.29 |
Reads mapping | ||||
Misassemblies | ||||
# misassemblies | 0 | 853 | 673 | 13227 |
# relocations | 0 | 536 | 483 | 12247 |
# translocations | 0 | 301 | 178 | 946 |
# inversions | 0 | 16 | 12 | 34 |
# misassembled contigs | 0 | 435 | 423 | 4213 |
Misassembled contigs length | 0 | 858930906 | 746258721 | 1368133947 |
# local misassemblies | 0 | 54331 | 24403 | 12317 |
# scaffold gap size mis. | 0 | 0 | 0 | 1 |
# structural variations | 0 | 624 | 411 | 589 |
# possible MGEs | 0 | 278 | 68 | 656 |
# unaligned mis. contigs | 0 | 112 | 237 | 1141 |
Unaligned | ||||
# fully unaligned contigs | 3 | 90 | 832 | 2710 |
Fully unaligned length | 603 | 2796488 | 22208176 | 35310322 |
# partially unaligned contigs | 0 | 2600 | 2193 | 6632 |
Partially unaligned length | 0 | 56219648 | 107778840 | 44985007 |
Mismatches | ||||
# mismatches | 0 | 7017301 | 15666952 | 5066741 |
# indels | 0 | 1843678 | 30384610 | 878984 |
Indels length | 0 | 17423151 | 49804606 | 9747856 |
# mismatches per 100 kbp | 0 | 258.95 | 580.26 | 184.06 |
# indels per 100 kbp | 0 | 68.03 | 1125.37 | 31.93 |
# indels (<= 5 bp) | 0 | 1237460 | 29537763 | 658785 |
# indels (> 5 bp) | 0 | 606218 | 846847 | 220199 |
# N's | 1119027 | 9 | 0 | 342197 |
# N's per 100 kbp | 38.36 | 0 | 0 | 11.87 |
Statistics without reference | ||||
# contigs | 2768 | 2879 | 3338 | 10211 |
# contigs (>= 0 bp) | 15304 | 2886 | 3392 | 11078 |
# contigs (>= 1000 bp) | 5547 | 2886 | 3385 | 11078 |
# contigs (>= 5000 bp) | 2152 | 2866 | 3262 | 8773 |
# contigs (>= 10000 bp) | 1583 | 2841 | 2972 | 5991 |
# contigs (>= 25000 bp) | 1196 | 2598 | 2393 | 2120 |
# contigs (>= 50000 bp) | 968 | 2199 | 1747 | 1269 |
Largest contig | 75724015 | 28413671 | 21995043 | 22430362 |
Total length | 2917182483 | 2763064770 | 2803317233 | 2882560136 |
Total length (>= 0 bp) | 2925908655 | 2763079553 | 2803418874 | 2884574069 |
Total length (>= 1000 bp) | 2921835836 | 2763079553 | 2803414118 | 2884574069 |
Total length (>= 5000 bp) | 2914852648 | 2763015671 | 2803010725 | 2876870677 |
Total length (>= 10000 bp) | 2911087860 | 2762827048 | 2800976242 | 2855802785 |
Total length (>= 25000 bp) | 2904606726 | 2758292768 | 2790665674 | 2796743012 |
Total length (>= 50000 bp) | 2896683228 | 2743715473 | 2767782601 | 2768179185 |
N50 | 8389762 | 3763377 | 4316080 | 5288590 |
N75 | 3936041 | 1667697 | 2073525 | 2576159 |
L50 | 95 | 197 | 191 | 162 |
L75 | 218 | 467 | 427 | 353 |
GC (%) | 40.87 | 40.88 | 40.65 | 40.64 |
K-mer-based statistics | ||||
K-mer-based completeness | 99.51 | 83.93 | 26.59 | 85.72 |
K-mer-based cor. length (%) | 99.3 | 81.44 | 90.16 | 62.56 |
K-mer-based mis. length (%) | 0 | 18.21 | 8.52 | 33.19 |
K-mer-based undef. length (%) | 0.7 | 0.35 | 1.32 | 4.25 |
# k-mer-based misjoins | 0 | 523 | 97 | 892 |
# k-mer-based translocations | 0 | 299 | 90 | 304 |
# k-mer-based 100kbp relocations | 0 | 828 | 289 | 604 |
Predicted genes | ||||
Similarity statistics | ||||
# similar correct contigs | 0 | 7 | 7 | 7 |
# similar misassembled blocks | 0 | 60 | 60 | 60 |
Plots:Cumulative lengthNxNAxNGxNGAxMisassemblies
|
||
0 1200 2400 3600 4800 6000 7200 8400 9600th contig 0 500 Mbp 1000 Mbp 1500 Mbp 2000 Mbp 2500 Mbp 3000 Mbp 3500 Mbp 4000 Mbp |
|
|
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 1 kbp.
- The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.
- There is two misassemblies of the same type around a short alignment (less than 6 kbp)
- The gap between two long flanking sequences on the sides of the short alignment is less than 6 kbp.
- The long flanking sequences both are on the same strand of the same chromosome of the reference genome.