Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,809,829 +A 4.5% coding (240/1503 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
*REL6063,809,8291.→A 4.5% 3.2 ‑0.7 ‑0.244coding (240/1503 nt)uhpBsensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  new base (0/2):  ref base (21/21):  total (21/23)
Fisher's exact test strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 6.54e-01

AGTAAACTACCGATCATCAATAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGTAAATCAGCAG  >  REL606/3809794‑3809864
                                    |                                    
aatAAACTACCGATCATCAATAACGGAAAATGGGtt                                       <  1:3755823/34‑1 (MQ=255)
aGTAAACTACCGATCATCAATAACGGAAAATGGGtt                                       >  1:7867195/1‑36 (MQ=255)
 gTAAACTACCGATCATCATTAACGGAAAATGGGTT.a                                     >  1:6164746/1‑36 (MQ=255)
 gTAAACTACCGATCATCAATAACGGAAAATGGGTT.a                                     <  1:1475151/36‑1 (MQ=255)
 gTAAACTACCGATCATCAATAACGGAAAATGGGTT.a                                     >  1:380618/1‑36 (MQ=255)
 gTAAACTACCGATCATCAATAACGGAAAATGGGTT.a                                     <  1:5446359/36‑1 (MQ=255)
 gTAAACTACCGATCATCAATAACGGAAAATGGGTT.a                                     <  1:4685903/36‑1 (MQ=255)
 gTAAACTACCGATCATCAATAACGGAAAATGGGTT.a                                     >  1:3766166/1‑36 (MQ=255)
    aaCTACCGATCATCAATAACGGAAAATGGGTT.AAa.c                                 <  1:1764634/36‑1 (MQ=255)
    aaCTACCGATCATCAATAACGGAAAATGGGTT.AAa.c                                 <  1:7042091/36‑1 (MQ=255)
    aaCTACCGATCATCAATAACGGAAAATGAGTT.AAa.c                                 <  1:1375752/36‑1 (MQ=255)
     aCTACCGATCATCAATAACGGAAAATGGGTT.AAa.cc                                <  1:839741/36‑1 (MQ=255)
      cTACCGATCATCAATAACGGAAAATGGGTT.AAa.ccg                               <  1:3973414/36‑1 (MQ=255)
        aCCGATCATCAATAACGGAAAATGGGTT.AAa.ccgac                             <  1:382181/36‑1 (MQ=255)
        aCCGATCATCAATAACGGAAAATGGGTT.AAa.ccgac                             <  1:3649349/36‑1 (MQ=255)
         ccGATCATCAATAACGGAAAATGGGTT.AAa.ccgacc                            <  1:3848517/36‑1 (MQ=255)
         ccGATCATCAATAACGGAAAATGGGTT.AAa.ccgacc                            <  1:1920026/36‑1 (MQ=255)
           gATCATCAATAACGGAAAATGGGTT.AAA.CCGACCGc                          >  1:607070/1‑36 (MQ=255)
            atcatcAATAACGGAAAATGGGTT.AAA.CCGACCGcc                         >  1:2631461/1‑36 (MQ=255)
              catcaATAACGGAAAATGGGTT.AAA.CCGACCGCCTg                       >  1:3228905/1‑36 (MQ=255)
                tcaATAACGGAAAATGTGTT.AAA.CCGACCAGCTGCg                     >  1:4959700/1‑36 (MQ=25)
                tcaATAACGGAAAATGGGTT.AAA.CCGACCGCCTGCg                     >  1:7465569/1‑36 (MQ=255)
                  aaTAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGtt                   >  1:7644809/1‑36 (MQ=255)
                  aaTAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGtt                   >  1:2309197/1‑36 (MQ=255)
                   aaaaCGAAAAAGGGGTA.AAC.CCGACCGCCTGCGTTa                  <  1:3620632/34‑1 (MQ=16)
                   aTAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTa                  >  1:5162566/1‑36 (MQ=255)
                   aTAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTa                  <  1:7898294/36‑1 (MQ=255)
                    tAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTAg                 >  1:711042/1‑36 (MQ=255)
                     aagggAAATTGGCTA.AAA.CCGACCGCCTGCGTTAGc                <  1:6879634/33‑1 (MQ=19)
                     aaCGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTAGc                >  1:4833825/1‑36 (MQ=255)
                     aaCGAAAAGTGGATA.AAC.CCGACCGCCTGCGTTAGc                <  1:997150/36‑1 (MQ=16)
                     aaCGAAAAAGGGGTA.AAA.CCGACCGCCTGCGTTAGc                <  1:6644462/36‑1 (MQ=21)
                      caagAAAAAGGGTT.AAACCCGACCGCCTGCGTTAGc                <  1:2167745/33‑1 (MQ=16)
                      acagAAAATGGGTT.AAA.CCTACCGCCTGCGTTAGcc               <  1:6890068/33‑1 (MQ=37)
                       cGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTAGCCa              >  1:730720/1‑36 (MQ=255)
                       agaaaaaTGGTTA.AAC.CCGACCGCCTGCGTTAGCCa              <  1:4286310/33‑1 (MQ=19)
                        ggAAAATGGGTT.AAA.CAGACCGCCTGCGTTAGCCAg             >  1:5594591/1‑36 (MQ=255)
                         gAAAATGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGt            >  1:4477350/1‑36 (MQ=255)
                         gAAAATGGGTT.AAA.CCGACCGCCGGCGTTAGCCAGt            >  1:4565989/1‑36 (MQ=255)
                         gAAAAAGGGTAAAAA.CGGCCCGCCTGCGTTAGCCAg             <  1:3084192/36‑1 (MQ=9)
                          aaaaTGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGTa           >  1:6572058/1‑36 (MQ=255)
                          aaaaGGGGTA.AAC.CCGACCGCCTGCGTTAGCCAGTa           <  1:7090262/36‑1 (MQ=25)
                           aaaTGGGTT.AAA.CCAAACGCCTGAGTTAGCCAGTaa          >  1:5663138/1‑36 (MQ=37)
                           aaaCGGGTTAAAA.CCGCCCGCCTGCGTTAGCCAGTa           <  1:1468525/36‑1 (MQ=16)
                            aaggggTA.AAA.CCGACCGCCTGCGTTAGCCAGTaaa         <  1:1319491/33‑1 (MQ=37)
                             aTGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGTAAAt        >  1:5071027/1‑36 (MQ=255)
                             aTGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGTAAAt        >  1:6790997/1‑36 (MQ=255)
                             aTGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGTAAAt        >  1:5976007/1‑36 (MQ=255)
                                ggTT.AAACCCGACCGCCTGCGTTAGCCAGTAAATca      <  1:7374693/36‑1 (MQ=37)
                                ggTT.AAA.CCGACCGCCTGCGTTAGCCAGTAAATcag     >  1:940564/1‑36 (MQ=255)
                                ggTT.AAA.CCCCCCGCCCGCGTTAGTCAGTAAATcgg     >  1:5802/1‑34 (MQ=16)
                                ggTA.AAC.CCGACCGCCTGCGTTAGCCAGTAAATcag     <  1:5295343/36‑1 (MQ=37)
                                  tt.AAA.CCGACCGCCTGCGTTAGCCAGTAAATcagca   >  1:3526105/1‑36 (MQ=255)
                                   t.AAA.CCGACCGCCTGCGTTAGCCAGTAAATcagcag  >  1:7610183/1‑36 (MQ=255)
                                    |                                    
AGTAAACTACCGATCATCAATAACGGAAAATGGGTT.AAA.CCGACCGCCTGCGTTAGCCAGTAAATCAGCAG  >  REL606/3809794‑3809864

Base quality scores:  ATCG  < 3 ≤  ATCG  < 6 ≤  ATCG  < 16 ≤  ATCG  < 29 ≤  ATCG  < 37 ≤  ATCG