Coverage score
For elongated data, error-corrected data, or data sets in which condensation was not used, the Coverage score is based on the adjusted coverage. Because reads near the 5’ end are more accurate than reads at the 3’ end, mismatches that are found at the at the beginning of a read are weighted more heavily than mismatches that are found in the 3’end of the read. As result, adjusted coverage is calculated according to the following:
Adjusted Coverage = 1.2*(1st 1/3 mismatch) + (2nd 1/3 mismatch) + 0.7*(3rd 1/3 mismatch)
and the Coverage score is then calculated according to the following:
Coverage Score = 8log10(Adjusted Coverage)
For example, consider a nucleotide with 200x coverage that has 100 reads with a mismatch:
• No mismatch = 100
• 1st 1/3 mismatch = 50
• 2nd 2/3 mismatch = 30
• 3rd mismatch = 20
• Normal coverage - 100 + 50 + 30 + 20 = 200
• Adjusted coverage = 100 +1.2(50) + 30 + 0.7(20) = 204x
For data sets in which consolidation was used, the Coverage score is based on the normal coverage and is calculated according to the following:
Coverage Score = 8log10(Normal Coverage)