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Update model.md
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@wang-q
wang-q committed Dec 2, 2024
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Expand Up @@ -524,29 +524,29 @@ bash 0_script/0_master.sh

Table: statInsertSize

| K | property | min | max |
|------|----------------------:|--------------|--------------|
| R.21 | Homozygous (a) | | 100% |
| K | property | min | max |
|------|-----------------------|-------------:|-------------:|
| R.21 | Homozygous (a) | | 100% |
| | Genome Haploid Length | | 4,478,083 bp |
| | Genome Repeat Length | 136,755 bp | 136,883 bp |
| | Genome Unique Length | 4,339,242 bp | 4,343,288 bp |
| | Model Fit | 97.2749% | 97.3934% |
| | Read Error Rate | | 0.531821% |
| | Kmer Cov | | 299.7 |
| R.51 | Homozygous (a) | | 100% |
| | Genome Repeat Length | 136,755 bp | 136,883 bp |
| | Genome Unique Length | 4,339,242 bp | 4,343,288 bp |
| | Model Fit | 97.2749% | 97.3934% |
| | Read Error Rate | | 0.531821% |
| | Kmer Cov | | 299.7 |
| R.51 | Homozygous (a) | | 100% |
| | Genome Haploid Length | | 4,385,263 bp |
| | Genome Repeat Length | 91,444 bp | 91,569 bp |
| | Genome Unique Length | 4,290,813 bp | 4,296,704 bp |
| | Model Fit | 97.3222% | 97.6265% |
| | Read Error Rate | | 0.326106% |
| | Kmer Cov | | 223.4 |
| R.81 | Homozygous (a) | | 100% |
| | Genome Repeat Length | 91,444 bp | 91,569 bp |
| | Genome Unique Length | 4,290,813 bp | 4,296,704 bp |
| | Model Fit | 97.3222% | 97.6265% |
| | Read Error Rate | | 0.326106% |
| | Kmer Cov | | 223.4 |
| R.81 | Homozygous (a) | | 100% |
| | Genome Haploid Length | | 4,304,378 bp |
| | Genome Repeat Length | 60,194 bp | 60,313 bp |
| | Genome Unique Length | 4,239,931 bp | 4,248,326 bp |
| | Model Fit | 96.7883% | 97.4791% |
| | Read Error Rate | | 0.272491% |
| | Kmer Cov | | 151.5 |
| | Genome Repeat Length | 60,194 bp | 60,313 bp |
| | Genome Unique Length | 4,239,931 bp | 4,248,326 bp |
| | Model Fit | 96.7883% | 97.4791% |
| | Read Error Rate | | 0.272491% |
| | Kmer Cov | | 151.5 |

Table: statFastK

Expand Down Expand Up @@ -720,50 +720,15 @@ Table: statUnitigsSuperreads.md

Table: statMRUnitigsSuperreads.md

| Name | CovCor | Mapped | N50Anchor | Sum | # | SumOthers | median | MAD | lower | upper |
|---------------|-------:|-------:|----------:|------:|----:|----------:|-------:|----:|------:|------:|
| Q0L0X40P000 | 40.0 | 0.988 | 33273 | 4.57M | 238 | 170.27K | 39 | 6 | 7 | 114 |
| Q0L0X40P001 | 40.0 | 0.988 | 28779 | 4.53M | 259 | 201.39K | 40 | 6 | 7.3 | 116 |
| Q0L0X40P002 | 40.0 | 0.988 | 30071 | 4.64M | 260 | 164.17K | 39 | 7 | 6 | 120 |
| Q0L0X80P000 | 80.0 | 0.986 | 17506 | 4.5M | 422 | 325.46K | 79 | 11 | 15.3 | 224 |
| Q0L0X80P001 | 80.0 | 0.985 | 14470 | 4.5M | 463 | 341.13K | 79 | 11 | 15.3 | 224 |
| Q0L0X80P002 | 80.0 | 0.985 | 15397 | 4.51M | 435 | 302K | 79 | 12 | 14.3 | 230 |
| Q25L60X40P000 | 40.0 | 0.989 | 32007 | 4.53M | 240 | 129.1K | 40 | 7 | 6.3 | 122 |
| Q25L60X40P001 | 40.0 | 0.989 | 30801 | 4.56M | 235 | 150.98K | 40 | 7 | 6.3 | 122 |
| Q25L60X40P002 | 40.0 | 0.989 | 29647 | 4.59M | 253 | 150.28K | 40 | 7 | 6.3 | 122 |
| Q25L60X80P000 | 80.0 | 0.99 | 21998 | 4.52M | 335 | 197.18K | 79 | 12 | 14.3 | 230 |
| Q25L60X80P001 | 80.0 | 0.99 | 24337 | 4.51M | 317 | 256.08K | 79 | 12 | 14.3 | 230 |
| Q25L60X80P002 | 80.0 | 0.99 | 22977 | 4.53M | 330 | 290.55K | 80 | 12 | 14.7 | 232 |
| Q30L60X40P000 | 40.0 | 0.987 | 29689 | 4.54M | 252 | 99.35K | 40 | 8 | 5.3 | 128 |
| Q30L60X40P001 | 40.0 | 0.987 | 28714 | 4.55M | 261 | 96.91K | 40 | 8 | 5.3 | 128 |
| Q30L60X40P002 | 40.0 | 0.986 | 30868 | 4.54M | 259 | 79.09K | 40 | 8 | 5.3 | 128 |
| Q30L60X80P000 | 80.0 | 0.988 | 34031 | 4.55M | 223 | 97.39K | 80 | 14 | 12.7 | 244 |
| Q30L60X80P001 | 80.0 | 0.988 | 34330 | 4.53M | 220 | 93.71K | 80 | 14 | 12.7 | 244 |

Table: statUnitigsTadpole.md

| Name | CovCor | Mapped | N50Anchor | Sum | # | SumOthers | median | MAD | lower | upper |
|-----------|-------:|-------:|----------:|------:|----:|----------:|-------:|----:|------:|------:|
| MRX40P000 | 40.0 | 0.973 | 66625 | 4.52M | 117 | 51.05K | 39 | 6 | 7 | 114 |
| MRX40P001 | 40.0 | 0.973 | 60759 | 4.52M | 123 | 55.8K | 39 | 6 | 7 | 114 |
| MRX40P002 | 40.0 | 0.974 | 73590 | 4.52M | 117 | 54.86K | 40 | 6 | 7.3 | 116 |
| MRX80P000 | 80.0 | 0.973 | 53662 | 4.51M | 143 | 71.55K | 79 | 10 | 16.3 | 218 |
| MRX80P001 | 80.0 | 0.972 | 55069 | 4.51M | 152 | 71.62K | 79 | 10 | 16.3 | 218 |
| MRX80P002 | 80.0 | 0.974 | 54812 | 4.51M | 146 | 64.84K | 79 | 9 | 17.3 | 212 |

Table: statMRUnitigsTadpole.md

| Name | Mapped | N50Anchor | Sum | # | SumOthers | median | MAD | lower | upper |
|-------------------------------|-------:|----------:|----:|--------:|----------:|-------:|----:|------:|------:|
| 7_merge_anchors | 78639 | 6.45M | 160 | 672.98K |
| 7_merge_mr_unitigs_bcalm | 78592 | 4.52M | 101 | 5.96K |
| 7_merge_mr_unitigs_bifrost | 78601 | 4.53M | 107 | 7.09K |
| 7_merge_mr_unitigs_superreads | 67346 | 4.52M | 111 | 6.81K |
| 7_merge_mr_unitigs_tadpole | 82766 | 4.52M | 100 | 45.75K |
| 7_merge_unitigs_bcalm | 63414 | 4.52M | 125 | 61.14K |
| 7_merge_unitigs_bifrost | 78639 | 4.52M | 111 | 58.34K |
| 7_merge_unitigs_superreads | 63418 | 4.54M | 124 | 21.15K |
| 7_merge_unitigs_tadpole | 59738 | 6.31M | 183 | 684.15K |
| Name | Mapped | N50Anchor | Sum | # | SumOthers | median | MAD | lower | upper |
|-------------------------------|-------:|----------:|----:|-------:|----------:|-------:|----:|------:|------:|
| 7_merge_anchors | 97548 | 4.54M | 101 | 0 |
| 7_merge_mr_unitigs_bcalm | 78592 | 4.52M | 101 | 5.96K |
| 7_merge_mr_unitigs_bifrost | 78601 | 4.53M | 107 | 7.09K |
| 7_merge_mr_unitigs_superreads | 67346 | 4.52M | 111 | 6.81K |
| 7_merge_unitigs_bcalm | 63414 | 4.52M | 125 | 61.14K |
| 7_merge_unitigs_bifrost | 78639 | 4.52M | 111 | 58.34K |
| 7_merge_unitigs_superreads | 63418 | 4.54M | 124 | 21.15K |

Table: statMergeAnchors.md

Expand All @@ -781,8 +746,9 @@ Table: statOtherAnchors.md
| Genome | 4641652 | 4.64M | 1 |
| Paralogs | 2003 | 260.35K | 131 |
| repetitive | 1235 | 91.99K | 169 |
| 7_merge_anchors.anchors | 78639 | 6.45M | 160 |
| 7_merge_anchors.others | 6032 | 672.98K | 294 |
| 7_merge_anchors.anchors | 97548 | 4.54M | 101 |
| glue_anchors | 105670 | 4.53M | 91 |
| fill_anchors | 110256 | 4.53M | 85 |
| spades.contig | 125607 | 4.58M | 140 |
| spades.scaffold | 132608 | 4.58M | 136 |
| spades.non-contained | 125607 | 4.56M | 75 |
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