The paper says the following:
Given a read of length m, BWA only tolerates a hit with at most k differences (mismatches or gaps), where k is chosen such that <4% of m-long reads with 2% uniform base error rate may contain differences more than k. With this configuration, for 15–37 bp reads, k equals 2; for 38–63 bp, k=3; for 64–92 bp, k=4; for 93–123 bp, k=5; and for 124–156 bp reads, k=6.
Can somebody explain me how the exact calculation is done?
best,
tefina
Given a read of length m, BWA only tolerates a hit with at most k differences (mismatches or gaps), where k is chosen such that <4% of m-long reads with 2% uniform base error rate may contain differences more than k. With this configuration, for 15–37 bp reads, k equals 2; for 38–63 bp, k=3; for 64–92 bp, k=4; for 93–123 bp, k=5; and for 124–156 bp reads, k=6.
Can somebody explain me how the exact calculation is done?
best,
tefina
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