Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,809,832 +C 18.7% coding (237/1503 nt) uhpB ← sensory histidine kinase in two‑component regulatory sytem with UhpA

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,809,8321.→C18.7% 6.5 ‑4.0 ‑0.116coding (237/1503 nt)uhpBsensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  new base (0/3):  ref base (11/2):  total (11/5)
Fisher's exact test strand distribution p-value = 1.79e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 8.91e-01

AAACTACCGATCATCAATAACGGAAAATGGGTTAAA.CCG.ACCGCCTGCGTTAGCCAGTAAATCAGCAGCC  >  REL606/3809797‑3809866
                                    |                                   
aaaCTACCGATCATCAATAACGGAAAATGGGTTaaa                                      <  1:5292970/36‑1 (MQ=255)
aaaCTACAGATCATCAATAACGGAAAATGGGTTaaa                                      <  1:5193234/36‑1 (MQ=255)
 aaCTACCGATCATCAATAACGGAAAATGGGTTAAa.c                                    >  1:4786399/1‑36 (MQ=255)
 aaCTACCGATCATCAATAACGGAAAATGGGTTAAa.c                                    >  1:3575439/1‑36 (MQ=255)
 aaCGACCGATCATCAATAACGGAAAATGGGTTAAa.c                                    >  1:5663575/1‑36 (MQ=255)
  aCTACCGATCATCAATAACGGAAAATGGGTTAAa.cc                                   >  1:1045251/1‑36 (MQ=255)
  aCTACCGATCATCAATAACGGAAAATGGGGTACa.cc                                   >  1:1011587/1‑36 (MQ=37)
    tACCGATCATCAATAACAGAAAACGGGATAAa.ccta                                 >  1:1919653/1‑34 (MQ=21)
     aCCGATGNNNGATCACGGGAAAGGGGTTAAa.ccg.ac                               <  1:1988228/36‑1 (MQ=9)
     aCCGATCATCAATAACGGAAAATGGGTTAAa.ccg.ac                               <  1:4341988/36‑1 (MQ=255)
      ccGATCATCAATAACGGAAAATGGGTTAAa.ccg.acc                              <  1:464105/36‑1 (MQ=255)
      ccGATCATCAATAACGGAAAATGGGTTAAa.ccg.acc                              <  1:5548463/36‑1 (MQ=255)
      ccGATCATCAATAACGGAAAATGGGTTAAa.ccg.acc                              <  1:2115312/36‑1 (MQ=255)
      aagATCATCAATAACGGAAAATGGGTTAAa.ccg.gcc                              <  1:2437055/34‑1 (MQ=38)
        gATCATCAATAACGGAAAATGGGTTAAA.CCG.ACCGc                            >  1:3360549/1‑36 (MQ=255)
        gATCAGCAATAAGGGAAAAAGGGTTAAA.CCG.ACCGc                            >  1:4993388/1‑36 (MQ=37)
         atcatcAATAACGGAAAATGGGTTAAA.CCG.ACCGcc                           >  1:2136230/1‑36 (MQ=255)
             tcaATAACGGAAAATGGGTTAAA.CCG.ACCGCCTGCg                       >  1:5879202/1‑36 (MQ=255)
               aaTAACGGAAAATGGGTTAAA.CCG.ACCGCCTGCGtt                     >  1:4247174/1‑36 (MQ=255)
                 tAACGGAAAATGGGTTAAA.CCG.ACCGCCTGCGTTAg                   >  1:5249182/1‑36 (MQ=255)
                  aaCGAAAAAGGGTTAAAA.CCG.ACCGCCTGCGTTAGc                  <  1:1631060/36‑1 (MQ=19)
                   aaggAAAAGGGGGTAAACCCG.TCCGCCTGCGTTAGc                  <  1:3683282/34‑1 (MQ=12)
                   aaggAAAAAGGGTTAAA.CCGAACCGCCTGCGTTAGc                  <  1:130947/34‑1 (MQ=18)
                       aaaaTGGGTAAAACCCG.ACCGCCTGCGTTAGCCAGt              <  1:4602328/36‑1 (MQ=25)
                       aaaaAGGGTTAAACCCG.ACCGCCTGCGTTAGCCAGt              <  1:5456651/36‑1 (MQ=25)
                        aaaTGGGTTAAA.CCG.ACCGCCTGCGTTAGCCAGTaa            >  1:5765553/1‑36 (MQ=255)
                        aaaTGGGTTAAA.CCG.ACCGCCTGCGTTAGCCAGCaa            >  1:2316782/1‑36 (MQ=255)
                         aaTGGGTTAAA.CCG.ACCGCCTGCGTTAGCCAGTaaa           >  1:4086053/1‑36 (MQ=255)
                            cggTTAAA.CCG.ACAGACTGCGTTAGCCCGTAAATca        >  1:2449705/2‑36 (MQ=25)
                              ataaaa.CCT.ACCGCCTGCGTTAGCCAGTAAATcagc      <  1:901732/33‑1 (MQ=37)
                                tAAA.CCG.ACCGCCTGCGTTAGCCAGTAAATcagcag    >  1:3897820/1‑36 (MQ=255)
                                  aa.CCG.ACCGCCTGCGTTAGCCAGTAAATCAGCAGcc  >  1:2758642/1‑36 (MQ=255)
                                    |                                   
AAACTACCGATCATCAATAACGGAAAATGGGTTAAA.CCG.ACCGCCTGCGTTAGCCAGTAAATCAGCAGCC  >  REL606/3809797‑3809866

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 16 ≤  ATCG  < 27 ≤  ATCG  < 37 ≤  ATCG