Rice FPC Map

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The rice genome is approximately 400Mb in size. CUGI was funded by Novartis to fingerprint and end sequence two deep-coverage BAC libraries from O.sativa ssp. japonica cv. Nipponbare rice. The HindIII and EcoRI BAC libraries are available from CUGI. The clones were digested with HindIII, run on agarose gels, band-called using Image, and automatically assembled at a 1e-12 using FPC. The anchored markers are from the Japanese RGP high density rice genetic map .

WebFPC Java display of contigs (WARNING IE USERS: Requires Java Plugin Get it!)
FTP **FPC files. Bands, sizes and gels not available.
Information on WebFPC, markers, clones and the FPC ftp file.

** The FPC file is in the new V7 format. Download the new FPC executable.

12 Sept 03 New release of Rice FPC
Contigs per Chromosome
Clones Cov Marker Anchor Contig Single 1 2 3 4 5 6 7 8 9 10 11 12
72703 25x 8870 2427 180 3276 8 5 17 10 10 3 3 3 5 9 14 9

The contigs have been merged by HyeRan Kim using IRGSP sequenced data and fixed discrepancy. Given an average band size of 4740.8 (calculated using sequence data of chr 1, 4 and 10), and the total length of all contigs is 79214 CB units, the contigs coverage approximately 377.5 MB, and the longer contig is approimately 17Mb (ctg56 on Chr7).
  • Integration displays information and contigs from the integraion of the Monsanto and AGI physical map data [Chen et al. (2002) Plant Cell 14:537-545].
  • Status shows the current WebFPC contig and the Integration contig for each sequenced clone. The Integration contigs are frozen, so you can always reference this page from now on to find a new contig number if the contig numbers have changed.

WebFPC has a feature that allows you to select a sequenced clones (ones that end in "sd1") and it pops up a window with the Genbank or Gramene record. Many of the markers also link to Gramene. Highlight a clone or marker, select Genbank or Gramene in the upper right pull-down, if the button below says "Lookup Current", then it exists in the corresponding database; select Lookup Current button. See the documentation for platforms its been tested on, other new features, and how to use.

Clone Description:

  • Clones starting with 'a' are from our HindIII library (AGI name OSJNBa).
  • Clones starting with 'b' are from our EcoRI library (AGI name OSJNBb).
  • Clones starting with 'OJ' are from Monsanto.
  • Clones starting with 'PAC' are from the RGP.
  • Clones ending with a '_cv' have been confirmed for sequencing (not all are confirmed clones have a _cv clone).
  • Clones with a 'sd1' are sequenced clones that have been digested using the Fsd program and entered into FPC. If a clone is larger than 150kb, its will be broken up into 80% overlapping clones numbered sd2, etc.

Sequenced Clones:

  • Yellow: SD clones (end with "sd1"), sequenced clones from genbank that have been digested. These clones have been placed in contigs by finding the highest hit based on a 1e-10 cutoff, and adding the clone in that position.
  • Gray: The corresponding AGI clone, if one exists.
  • Orange: Clones that have been selected from sequencing, but are not submitted to Genbank.


  • The anchored markers (shown along the bottom of each contig) are from the Japanese high density linkage map. Most of the rest of the markers are from hybridization. A remark is associated with each clone that has marker results from an external laboratory, except for the following two sets:
  • Cornell and JRGP oryza sativa genetic markers were added using information provided by Gramene. These markers were run against BAC genomic sequence using BLAT, and added based on a set of filters. All electronic markers have type eMrk and are colored yellow in WebFPC. Clones hitting existing markers have one of the following remarks:
    • Electronic by Gramene (marker-name) -- Existing marker added to this clone
    • eConfirmed by Gramene (marker-name) -- Existing marker was already attached to this clone
    This dataset provides 3902 new markers (7444 clone hits), and 1446 new clone attachments to existing markers.
  • SOG and AOG markers are overgos from the Andrew Paterson's lab at University of Georgia - Athens. They are derived from probes that have been mapped in maize and other grasses. Markers with prefixes AEST, BCD, BNL, CDO. CDSB, SDSC, CDSR, CSU, HHU, PHY, RG, RZ, PRC, PSB, and PSHR are plasmids that have been mapped by Paterson's lab as well.
    The overgos provide 1581 new markers (32337 clone hits).
    The plasmids provide 104 new markers (3571 clone hits), 113 new clone attachments to existing markers, and 14 confirmations of clone attachments.

Notes on FPC file:

1. FPC has a function to add remark to each contig that is anchored or has sequenced clones. The function counts the number of anchors and the number of SD (simulated digest ) clones. It then determines what chromosome the anchors and sequence are from; for the sequence, the chromosome has been parsed from the Genbank entry and entered as a remark. The contig remark below says 5 items (anchor or sequence) are to Chr1, and 1 item is on Chr6. Two of the items are frameworks (i.e. anchors, genetic markers) and 4 are sequence.

     e.g.      Chr1 [5 Chr6-1 Fw2 Seq4]
2. There is one contig with a status of Dead, these are chloroplast clones.
3. Clones that start with a "!" are cancelled. The clone count above does not include cancelled clones or clones from a Dead contig.


Chen, M., Presting, G., Barbazuk, W., Goicoechea, J., Blackmon, B., Fang, G., Kim, H., Frisch, D., Yu, Y., Higingbottom, S., Phimphilai, J., Phimphilai, D., Thurmond, S., Gaudette, B., Li, P., Liu, J., Hatfield, J., Sun, S., Farrar, K., Henderson, C., Barnett, L., Costa, R., Williams, B., Walser, S., Atkins, M., Hall, C., Bancroft, I., Salse, J., Regad, F., Mohapatra, T., Singh, N., Tyagi, A., Soderlund, C., Dean, R., and Wing, R. (2002). An integrated physical and genetic map of the rice genome. / Plant Cell/.

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