Pangenome order that are not integer.

[Jilong-Jerome]

Hi John,

Great thanks for the super useful and beautiful GENESPACE for visualising genome synteny.

I did a successful run with the GENESPACE for 6 de novo assemblies. I find that in the output of pangenomeDB file, the pangenome order (pgOrd) is not always integer. It doesn't matter much with ploting using pgOrd as a coordinate, but I had a hard time understanding what a pgOrd of 133.5 or 133.75 could mean.

For example, the second column is the pgOrd in the generated pangenomeDB.

LIN.HiC_1 133 27 3226 3_30560 FALSE MIM FALSE FALSE FALSE TRUE MIM.HiC_15_file_1_file_1_jg681 LIN.HiC_1 133 27 3226 5_5110 FALSE TENT FALSE FALSE FALSE TRUE TENT.HiC_3_file_1_file_1_jg1471 LIN.HiC_1 133.5 28 28926 1_10909 TRUE DUM FALSE FALSE TRUE FALSE DUM.HiC_4_file_1_file_1_jg1258 LIN.HiC_1 133.5 28 28926 0_15238 FALSE BI FALSE FALSE FALSE TRUE BI.HiC_7_file_1_file_1_jg128 LIN.HiC_1 133.5 28 28926 0_16066 FALSE BI FALSE FALSE FALSE TRUE BI.HiC_7_file_1_file_1_jg950 LIN.HiC_1 133.5 28 28926 0_17444 FALSE BI FALSE FALSE FALSE TRUE BI.HiC_7_file_1_file_1_jg2324 LIN.HiC_1 133.5 28 28926 3_20080 FALSE MIM FALSE FALSE FALSE TRUE MIM.HiC_9_file_1_file_1_jg217 LIN.HiC_1 133.5 28 28926 4_6206 FALSE SARA FALSE FALSE FALSE TRUE SARA.HiC_2_file_1_file_1_jg1508 LIN.HiC_1 133.75 29 39572 3_3964 TRUE MIM FALSE FALSE TRUE FALSE MIM.HiC_2_file_1_file_1_jg1647 LIN.HiC_1 133.75 29 39572 5_11775 FALSE TENT FALSE FALSE FALSE TRUE TENT.HiC_5_file_1_file_1_jg1103

I really appreciate if you can elaborate it a bit on how the pgOrd is defined.

Best, Jilong

[jtlovell]

Yes, in short. pgOrd can be an integer, but not necessarily. It is the interpolated gene order, using neighboring syntenic anchors. It is typically a non-integer when that orthogroup does not have a member in the reference genome.

[Jilong-Jerome]

Thanks for the clarification !