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July 26, 2020 21:41
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A note on evaluating genome assemblies with CHM13 BACs
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| + bash getStats.sh chm13_pergrine_p_ctg_cns.fasta | |
| Checking attempted with maximum distance from contig end of 1000 bp..Done | |
| ******************* BAC SUMMARY ****************** | |
| TOTAL : 341 | |
| BP : 51532183 | |
| ************** Statistics for: chm13_p_ctg_cns.fasta **************** | |
| BACs closed: 321 (94.1349); BACs attempted: 333 %good = 96.3964; BASES 48527269 (94.1689) | |
| Median: 99.9878 | |
| MedianQV: 39.1364 | |
| Mean: 99.94864 | |
| MeanQV: 32.89382 | |
| ***** STATS IGNORING INDELS ******************** | |
| Median: 100 | |
| MedianQV: Inf | |
| Mean: 99.99481 | |
| MeanQV: 42.84986 | |
| ********************************************** | |
| + bash getStats.sh chm13_20k_hicanu_hifi.fasta | |
| Checking attempted with maximum distance from contig end of 1000 bp..Done | |
| ******************* BAC SUMMARY ****************** | |
| TOTAL : 341 | |
| BP : 51532183 | |
| ************** Statistics for: chm13_20k_hicanu_hifi.fasta **************** | |
| BACs closed: 326 (95.6012); BACs attempted: 338 %good = 96.4497; BASES 49196764 (95.468) | |
| Median: 99.9915 | |
| MedianQV: 40.70581 | |
| Mean: 99.95299 | |
| MeanQV: 33.27811 | |
| ***** STATS IGNORING INDELS ******************** | |
| Median: 100 | |
| MedianQV: Inf | |
| Mean: 99.99075 | |
| MeanQV: 40.33714 | |
| ********************************************** | |
| + bash getStats.sh CHM13-r251.p_ctg.fasta | |
| Checking attempted with maximum distance from contig end of 1000 bp..Done | |
| ******************* BAC SUMMARY ****************** | |
| TOTAL : 341 | |
| BP : 51532183 | |
| ************** Statistics for: CHM13-r251.p_ctg.fasta **************** | |
| BACs closed: 314 (92.0821); BACs attempted: 336 %good = 93.4524; BASES 47494297 (92.1643) | |
| Median: 99.99105 | |
| MedianQV: 40.48177 | |
| Mean: 99.90872 | |
| MeanQV: 30.39602 | |
| ***** STATS IGNORING INDELS ******************** | |
| Median: 100 | |
| MedianQV: Inf | |
| Mean: 99.98409 | |
| MeanQV: 37.98325 | |
| ********************************************** |
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