GemSIM: general, error-model based simulator of next-generation sequencing data

BMC Genomics

Table 4 Number of genomic sites considered by VarScan for increasing values of M.A.Q

M.A.Q.	Illumina v4	Illumina v5	Roche/454
10	416376	416380	416374
11	416376	416380	416374
12	416376	416380	416372
13	416376	416380	416370
14	416376	416380	416369
15	416376	416380	416368
16	416376	416380	416365
17	416376	416380	416361
18	416376	416380	416357
19	416376	416378	416357
20	416376	416378	416353
21	416376	416378	416353
22	416376	416378	416349
23	416375	416378	416345
24	416375	416378	416340
25	416375	416378	416336
26	416375	416378	416328
27	416375	416378	416323
28	416375	416377	416317
29	416375	416377	416312
30	416375	416377	416303
31	416374	416377	416292
32	416372	416376	416284
33	416371	416376	416271
34	416368	416376	416260
35	14370	416376	416251
36	0	416375	416233
37	0	416375	416226
38	0	416374	416110
39	0	416368	416076
40	0	416358	415943

M.A.Q gives the minimum quality a base within a read must have for VarScan to 'count' it. At each position with the genome, there must be at least 100 bases (from 100 reads) with a quality above the value of M.A.Q, for the genomic position to be considered by VarScan when scanning for SNPs. For example, a value of zero means there were no sites within the reference genome where there were more than 100 aligned bases with a quality score greater than the specified M.A.Q.

ISSN: 1471-2164