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Old 12-09-2009, 02:35 AM   #1
m_elena_bioinfo
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Location: Ospedali Riuniti di Bergamo, ITALY

Join Date: Oct 2009
Posts: 99
Default MAQ output format

Hi users,
I have some questions about MAQ output file (.snp, generated from cns file), like this:

hsa-mir-1308 23 C T 27 1 0.00 27 24
N 3 N
hsa-mir-1975 31 A R 107 14 1.00 63 62
A 114 G
hsa-mir-1975 62 G R 27 3 1.00 63 30
G 35 A
hsa-mir-1977 57 T Y 18 11 1.00 63 12
T 255 C
hsa-mir-21 38 T G 17 1 0.00 27 4
N 13 N
hsa-mir-23b 90 A G 15 2 0.00 27 0
A 12 R
hsa-mir-26a-2 36 G C 19 2 0.00 27 16
G 8 S
hsa-mir-26a-2 37 T G 17 2 0.00 27 18
T 6 K
hsa-mir-26a-2 45 T C 33 2 0.00 27 0
N 15 N
hsa-mir-30c-1 50 A G 4 1 0.00 4 0
N 26 N

- What is the "read depth" in 6th column?

- How can I know how many times MAQ counts the mutations (in other words, how many
times a base call occurs in a specific position)?

- To find INDELs, (and put them in the output), is there any specific commands?

- What are the 8th and 9th columns? Are quality parameters?

Thank you very much,
Maria Elena
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