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rmcolq
change in coverage mid-gene
I have two Klebsiella pneumoniae isolates I'm looking at (KN0056-F and KN0056-L) that are basically identical according to snippy (4 SNPs different). I found this change in coverage reported in the Pandora output:
acs 759 . GA TA . . SVTYPE=PH_SNPs;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:26,0:19,0:26,0:19,0:105,0:79,0:0,1:-6.07005,-267.233:261.163 0:42,0:32,0:43,0:32,0:171,0:131,0:0,1:-11.5429,-428.783:417.24
acs 801 . C A . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:21,0:15,0:21,0:15,0:87,0:61,0:0,1:-3.27659,-225.786:222.51 0:33,0:31,0:33,0:31,0:134,0:127,0:0,1:-6.98006,-382.731:375.751
acs 828 . C T . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:13,0:8,0:16,0:9,0:54,0:32,0:0.25,1:-11.455,-156.709:145.254 0:22,0:20,0:27,0:25,0:90,0:83,0:0.25,1:-13.8359,-281.417:267.581
acs 852 . T C . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:12,0:3,0:14,0:4,0:63,0:18,0:0,1:-6.88131,-129.078:122.196 0:22,0:19,0:24,0:19,0:113,0:95,0:0,1:-2.88244,-276.812:273.93
acs 900 . A T . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=2;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 1:0,2:0,0:0,2:0,0:0,6:0,0:1,1:-69.2103,-53.8908:15.3196 1:0,9:0,13:0,9:0,13:0,29:0,40:1,0:-189.314,-9.21901:180.095
acs 951 . A G . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=1;AN=1 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-60,-60:0 1:0,1:0,3:0,1:0,3:0,6:0,15:1,0.5:-106.421,-54.0413:52.3794
acs 961 . T C . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=1;AN=1 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:0,0:0,0:0,0:0,0:0,0:0,0:1,1:-60,-60:0 1:0,0:0,1:0,0:0,0:0,5:0,9:1,0.833333:-92.6052,-76.8825:15.7227
acs 996 . A G,T . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=1,0;AN=1 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF .:0,0,0:0,0,0:0,0,0:0,0,0:0,0,0:0,0,0:1,1,1:-60,-60,-60:0 1:0,4,0:0,5,0:0,6,0:0,8,0:0,14,0:0,16,0:1,0.333333,1:-129.447,-37.4108,-129.447:92.0357
acs 1112 . C T . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:22,0:27,0:22,0:27,0:45,0:54,0:0,1:-7.90707,-285.653:277.746 0:35,0:33,0:35,0:33,0:71,0:67,0:0,1:-8.63155,-401.152:392.52
acs 1143 . C T . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:30,0:31,0:32,0:31,0:120,0:126,0:0,1:-15.266,-340.915:325.649 0:27,0:27,0:36,0:35,0:111,0:108,0:0.25,1:-14.9739,-336.679:321.705
acs 1161 . C T . . SVTYPE=SNP;GRAPHTYPE=NESTED;AC=0;AN=2 GT:MEAN_FWD_COVG:MEAN_REV_COVG:MED_FWD_COVG:MED_REV_COVG:SUM_FWD_COVG:SUM_REV_COVG:GAPS:LIKELIHOOD:GT_CONF 0:30,0:32,0:32,0:32,0:152,0:161,0:0,1:-15.9919,-345.521:329.529 0:14,0:14,0:0,0:0,0:73,0:71,0:0.6,1:-32.3324,-216.945:184.612
When I look at this gene in the de novo assemblies, they are identical except at one position:
Query 1141 CGCATTCTTGGCTCGGTCGGCGAACCGATTAACCCGGAAGCCTGGGAGTGGTACTGGAAG 1200
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Sbjct 1141 CGCATTCTTGGCTCGGTCGGCGAACCGATTAACCCGGAAGCCTAGGAGTGGTACTGGAAG 1200
There is a big drop in coverage for three positions where KN0056-F has not been genotyped (zero coverage). The biggest problem being that this flags as a difference between these isolates when there shouldn't be.
There are regions in this gene (1959 bp long) that look like they are repeated in both the isolate genomes and also in the pandora reference. Pandora was run only with Illumina data.
The Pandora output files are here: /hps/nobackup/iqbal/leandro/klebs_neonate_leah/pandora_compare_results
The de novo assemblies are here (also raw reads): /hps/nobackup2/iqbal/projects/pandora/klebs/neonate/data/KpST17_Norway_20190617/contigs/patient-pairs
