Description

The CHROM record contains the coordinate information for each chromatin segment. Is also present information about the DNA sequence, such as the presence of a CTCF-binding motif together with its orientation. There is also the genomic position in bp and the variance of the observed spatial distribution.

Record Format

COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   "CHROM "
 8 - 15        Integer       serial       Bead serial number.
17 - 18        String        chrType      Chromatin type for the bead
20 - 25        String        DNAprop      DNA properties
27 - 30        String        chainID      Chain identifier
32 - 39        Integer       beadSeq      Bead sequence number into a chain
41 - 48        Real(8.3)     x            Orthogonal coordinates for X
50 - 57        Real(8.3)     y            Orthogonal coordinates for Y
59 - 66        Real(8.3)     z            Orthogonal coordinates for Z
68 - 77        Integer       startDis     Start of genomic position for that bead
79 - 88        Integer       endDis       End of genomic position for that bead
90 - 97        Real(8.3)     varDist      Variance of the observed spatial distribution

Details

• The serial number starts at 1 for the first coordinate of the model and goes sequentially until ENDMDL record. beadSeq identifies the order of the beads within a certain chain.
• chainID is the same as specified at SEQCHR record.
• The unit for coordinates is specified in LENGTH record.
• Start and end of genomic position for the bead specify, in base pair, the genomic range for the locus represented by that bead, according to the indicated resolution at MASTER record.
• The variance of the observed spatial distribution is specially important in the case of experimental data. For data generated by simulations, this field can the set as 1.000.
• The list of CHROM records in a chain is terminated by a TER record.
• If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.

Examples

         1         2         3         4         5         6         7         8         9        10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL         1
CHROM         1 B3        C1          1  370.891  366.965  369.383          1      50000    1.000
CHROM         2 B3        C1          2  370.929  367.777  369.942      50001     100000    1.000
CHROM         3 B3        C1          3  370.836  368.751  369.875     100001     150000    1.000
CHROM         4 B3        C1          4  371.239  369.019  369.061     150001     200000    1.000
CHROM         5 B3        C1          5  371.711  368.817  368.213     200001     250000    1.000

         1         2         3         4         5         6         7         8         9        10
1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890
CHROM       251 A2        C1        251  372.254  367.706  367.152   12500001   12550000    1.000
CHROM       252 A2 ctcf+  C1        252  371.429  367.220  367.216   12550001   12600000    1.000
CHROM       253 A2        C1        253  371.107  368.054  367.538   12600001   12650000    1.000
CHROM       254 A2        C1        254  370.272  368.131  367.116   12650001   12700000    1.000
CHROM       255 A2 ctcf-  C1        255  369.712  368.117  366.246   12700001   12750000    1.000
CHROM       256 B1        C1        256  370.170  368.201  365.397   12750001   12800000    1.000
CHROM       257 B3        C1        257  370.760  367.578  364.993   12800001   12850000    1.000
CHROM       258 B3        C1        258  370.218  366.877  365.463   12850001   12900000    1.000
CHROM       259 B3        C1        259  369.322  367.104  365.775   12900001   12950000    1.000
CHROM       260 B3        C1        260  368.421  366.942  365.940   12950001   13000000    1.000
CHROM       261 B3        C1        261  367.892  366.505  365.209   13000001   13050000    1.000
CHROM       262 B3        C1        262  368.340  366.332  364.325   13050001   13100000    1.000