Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,809,832 +C 13.3% 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.→C13.3% 9.6 ‑2.3 0.030coding (237/1503 nt)uhpBsensory histidine kinase in two‑component regulatory sytem with UhpA
Reads supporting (aligned to +/- strand):  new base (0/4):  ref base (15/11):  total (15/15)
Fisher's exact test strand distribution p-value = 9.96e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

AAACTACCGATCATCAATAACGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATCAGCAGCCA  >  REL606/3809797‑3809867
                                      |                                    
aaaCTACCGATCATCAATAACGGAAAATGGGT.T.aaa                                       >  1:4964569/1‑36 (MQ=255)
aaaCTACCGATCATCAATAACGGAAAATGGGT.T.aaa                                       >  1:744087/1‑36 (MQ=255)
aaaCTACCGATCATCAATAACGGAAAATGGGT.T.aaa                                       >  1:3541193/1‑36 (MQ=255)
aaaCTACCGATCATCAATAACGGAAAATGGGT.T.aaa                                       <  1:6163000/36‑1 (MQ=255)
 aaCTACCGATCATCAATAACGTAAAATGGGT.T.AAa.c                                     <  1:7040669/36‑1 (MQ=255)
 aaCTACCGATCATCAATAACGGTAAACGGGT.T.AAa.c                                     >  1:7730781/1‑36 (MQ=37)
  aCTACCGATCATCAATAACGGAAAATGGGT.T.AAc.cc                                    <  1:3333841/36‑1 (MQ=255)
  aCTACCGATCATCAATAACGGAAAATGGGT.T.AAa.cc                                    <  1:4389842/36‑1 (MQ=255)
  aCTACCGATCATCAATAACGGAAAATGGGT.T.AAa.cc                                    <  1:5483219/36‑1 (MQ=255)
  aCTAACGATCATCAATAACGGAAAATGGGT.T.AAa.cc                                    <  1:7676897/36‑1 (MQ=255)
    tACCGATCATCAATAACGGAAACTGGGT.T.AAa.ccga                                  >  1:488411/1‑36 (MQ=255)
     acagATCATCAATAACGTAAAATTTGT.T.AAa.ccga.c                                <  1:1621252/33‑1 (MQ=16)
     aCCGATCATCAATAACGGAAAATGGGT.T.AAa.ccga.c                                >  1:3948620/1‑36 (MQ=255)
      ccGATCATCAATAACGGAAAATGGGT.T.AAa.ccga.cc                               <  1:2644015/36‑1 (MQ=255)
      ccGATCATCAATAACGGAAAATGGGT.T.AAa.ccga.cc                               <  1:2086957/36‑1 (MQ=255)
         atcatcAATAACGGAAAATGGGT.T.AAA.CCGA.CCGcc                            >  1:5525557/1‑36 (MQ=255)
               aaTAACGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGtt                      >  1:4535430/1‑36 (MQ=255)
               aaTAACGGAAAATGGGG.T.AAA.CCGA.CCGCCTGCGtt                      >  1:5882105/1‑36 (MQ=255)
                aTAACGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTa                     >  1:5528270/1‑36 (MQ=255)
                 tAACGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAg                    >  1:719440/1‑36 (MQ=255)
                 acaCGGAAAAGGGGT.A.AAC.CGGA.CCGCCTGCGTTAg                    <  1:7932541/34‑1 (MQ=16)
                  aaCGAAAAATGGTT.A.AAC.CCGA.CCGCCTGCGTTAGc                   <  1:1230881/36‑1 (MQ=16)
                   aCGGAAAATGGGT.T.AAC.CCGA.CCGCCTGCGTTAGcc                  <  1:986652/36‑1 (MQ=255)
                   aCGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGcc                  >  1:3318900/1‑36 (MQ=255)
                   aCGAAAAAGGGGT.A.AAA.CCGA.CCGCCTGCGTTAGcc                  <  1:174059/36‑1 (MQ=21)
                    cgaaaaaGGGGT.A.AAA.CCGA.CCGCCTGCGTTAGCCa                 <  1:5338833/33‑1 (MQ=21)
                    cGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCa                 <  1:501273/36‑1 (MQ=255)
                    cGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCa                 >  1:5177762/1‑36 (MQ=255)
                     ggAAAATGGGT.T.AAA.CCGA.CCGCCGGCGTTCGccgg                >  1:1538044/1‑34 (MQ=37)
                      gAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGt               >  1:3832803/1‑36 (MQ=255)
                      gAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGt               >  1:5481090/1‑36 (MQ=255)
                      gAAAAGGGGG.A.AAACCCGC.CCGCCTGCGTTAGCCAg                <  1:3678034/36‑1 (MQ=9)
                      aaaagTGGTT.A.AAA.CCGG.CCGCCTGCGTTAGCCAGt               <  1:5369817/35‑1 (MQ=16)
                      aaaaaAGGGTAT.AAACCCGC.CCGCCTGCGTTAGCCa                 <  1:4411080/35‑1 (MQ=9)
                       aaaaAGGTT.T.AAA.CCCACCCGCCTGCGTTAGCCAGt               <  1:7126473/36‑1 (MQ=16)
                       aaaaAGGGT.TAAAA.CCGA.CCGCCTGCGTTAGCCAGt               <  1:2696107/36‑1 (MQ=25)
                         aaTGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGTaaa            >  1:5627577/1‑36 (MQ=255)
                          aTGGGT.T.AAA.CCCA.CCGCCTGCGTTAGCCAGTAAAt           >  1:1275828/1‑36 (MQ=255)
                           agggA.T.AAACCCGA.CCGCCTGCGTTAGCCAGTAAAt           <  1:4243166/35‑1 (MQ=25)
                            gggT.T.AAACCCGG.CCGCCTGCGTTAGCCAGTAAATc          <  1:7438966/36‑1 (MQ=25)
                            gggT.A.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATca         <  1:7849172/36‑1 (MQ=255)
                             ggT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATcag        >  1:3502987/1‑36 (MQ=255)
                             ggT.A.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATcag        <  1:6826804/36‑1 (MQ=255)
                              gT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATcagc       >  1:7218476/1‑36 (MQ=255)
                               t.t.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATcagca      >  1:4667265/1‑36 (MQ=255)
                                 taaaa.CCGA.CCGCCTGCGTTAGCCAGTAAATcagca      <  1:6578034/34‑1 (MQ=255)
                                 taaaa.CCGA.CCGCCTGCGTTAGCCAGTAAATcagca      <  1:7077389/34‑1 (MQ=255)
                                  aaaa.CCGA.CCTCCTGCGTTAGCCAGTAAATcagcag     <  1:141733/35‑1 (MQ=255)
                                  aaaa.CCAC.CCGCCTGCGTTAGCCAGTAAATcagcag     <  1:2988638/35‑1 (MQ=25)
                                   aaa.CCGA.CCACCTCAGTTAGCCAGTAAATcagcatc    >  1:2650612/1‑34 (MQ=18)
                                    aa.CCGA.CCGCCTGCGTTAGCCAGTAAATCAGCAGcc   >  1:4038266/1‑36 (MQ=255)
                                     a.ccga.ccgCCTGCGTTAGCCAGTAAATCAGCAGCCa  >  1:4960983/1‑36 (MQ=255)
                                     a.ccga.ccgCCTGCGTTAGCCAGTAAATCAGCAGCCa  >  1:2072602/1‑36 (MQ=255)
                                     a.ccga.ccgCCTGCGTTAGCCAGTAAATCAGCAGCCa  >  1:1204796/1‑36 (MQ=255)
                                      |                                    
AAACTACCGATCATCAATAACGGAAAATGGGT.T.AAA.CCGA.CCGCCTGCGTTAGCCAGTAAATCAGCAGCCA  >  REL606/3809797‑3809867

Base quality scores:  ATCG  < 3 ≤  ATCG  < 6 ≤  ATCG  < 17 ≤  ATCG  < 29 ≤  ATCG  < 37 ≤  ATCG