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Table 5 Read mapping statistics

From: De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads

Read category WGA Unamplified
Assembly WGA Final WGA Final
Read count 1,362,775 1,362,775 2,137,475 2,137,475
Mapped 1,106,671 1,233,514 1,525,846 1,922,031
Well mapped1 571,180 727,433 563,302 1,386,713
Uniquely mapped2 16,977 143,820 16,568 412,753
Median mapped read proportion3 91.1% 94.1% 65.6% 96.7%
Median mapped proportion excluding well-mapped reads 56.1% 65.9% 31.1% 67.2%
  1. The number of reads that were generated from the WGA DNA and that mapped to either the assembly made from those reads (WGA) or from those generated from unamplified DNA (Final) are shown in columns 2 and 3. The number of reads that were generated from unamplified DNA (Unamplified) and that mapped to either the assembly made from the WGA reads (WGA), or from those generated from unamplified DNA (Final) are shown in columns 4 and 5. Since a similar fraction of WGA and unamplified reads do not map to the final assembly (approximately 10%), it appears that contaminating DNA was effectively removed (see ‘Methods’ for details). While the figure for the mapping of reads from the unamplified DNA to the WGA assembly is comparatively low, it is higher than the equivalent comparison of the completeness of genomes (100 × [completeness WGA/completeness final]), which is closer to 55% for Nanopolished assemblies (not shown), or 32.4% by stringent pairwise mapping. The difference is explained by redundant mapping of haplotype-specific and repeat-containing reads from the unamplified DNA
  2. WGA whole-genome amplification
  3. 1Reads that map at least 90% of their length to the reference assembly
  4. 2Reads that map only to the target assembly, and not the other assembly
  5. 3Median proportion of individual reads that aligned to the reference assembly