CpG_chrm

CpG_beg

CpG_end

address_A

address_B

target

nextBase

channel

Probe_ID

lastBase_A

mapFlag_A

mapChrm_A

mapPos_A

mapQ_A

mapCigar_A

mapSeq_A

mapNM_A

mapAS_A

mapYD_A

lastBase_B

mapFlag_B

mapChrm_B

mapPos_B

mapQ_B

mapCigar_B

mapSeq_B

mapNM_B

mapAS_B

mapYD_B

design

mask

(1-3) CpG_chrm, CpG_beg, CpG_end: genomic coordinate for the target, length 2 for CpG, length 1 for SNP and CpH. beg is 0-based and end is 1-based like in bed files.
(4-5) address_A, address_B: Chip/tango address for A-allele and B-allele.
(6) target: CG if the probe measures CpG methylation, reference allele if otherwise
(7) nextBase: the actual extension base (on the probe strand). "R" (stands for G/A) for Infinium-II probes
(8) channel: color channel, green or red
(9) Probe_ID: the probe ID
(10-19) lastBase_A, mapFlag_A, mapChrm_A, mapPos_A, mapQ_A, mapCigar_A, mapSeq_A, mapNM_A, mapAS_A, mapYD_A:
Mapping information for allele A. NM is the number of mutations. AS represents alignment score. YD (f/r/n) represents the bisulfite strand. mapFlag can be used to determine direction of the probe sequence. 0 means upstream and 16 means downstream.
(20-29) lastBase_B, mapFlag_B, mapChrm_B, mapPos_B, mapQ_B, mapCigar_B, mapSeq_B, mapNM_B, mapAS_B, mapYD_B:
Mapping information for allele B. Same as allele A.
(30) design: design group
(31) type: Infinium-I or Infinium-II