Determine N50 for fragments of 10 kb, 20 kb,25 kb, 30 kb, 45 kb, 60 kb,...

Determine N50 for fragments of 10 kb, 20 kb,25 kb, 30 kb, 45 kb, 60 kb, 65 kb, showing your working. Explain your result in terms of genome quality.

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Expert Solution

N50 determines the contig or the genomic fragment length that is needed to cover 50% of an organism's genome. The calculation of N50 involves the following steps:

1. Arranging genomic fragments based on their lengths from highest to lowest. Here, it will hence be arranged as:

65 kb>60 kb>45 kb>30 kb>25 kb>20 kb>10 kb

2. Summing the genomic fragments and halving the value will give us a number. The fragment to which this number will correspond will determine our N50 Value.

Sum of all the fragments here = 255 kb. Halving that value is 127.5 kb. Now starting from the beginning, 65+60=125 but 127.5 is greater than that. Again, 65+60+45=170, and 127.5 lies in this value.. So 45 kb is our N50 value.. The calculation can be better comprehended through the diagram that is attached along with.

A bigger N50 value is always better. 45 kb N50 value determines moderate genome quality. If we would have large contig sizes then the N50 value could have been greater and hence would reflect a better genome quality. Smaller N50 value indicates that there are not so many biologically significant contigs that could be generated by the fragmentation of the genome and the genome consists of small little contigs that do not carry much biological importance. Therefore 45 kb N50 is implicative of a moderate genome quality as there can be values above it.

gladiator answered 1 year ago

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