Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 452,245 T→A 22.2% Y44F (TAC→TTC)  hha ← modulator of gene expression, with H‑NS

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL606452,2450T→A22.2% 6.9 ‑3.8 ‑0.030131hhamodulator of gene expression, with H‑NS
Reads supporting (aligned to +/- strand):  new base (0/7):  ref base (12/10):  total (13/17)
Fisher's exact test strand distribution p-value = 2.30e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 9.27e-01

TGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAA  >  REL606/452210‑452273
                                   |                            
tGGTCAATTCGGCGAGGCGGTGATCTGCGGGTGAGt                              >  1:7837554/1‑36 (MQ=255)
tGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGGGt                              >  1:1723891/1‑36 (MQ=255)
tGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGt                              <  1:977441/36‑1 (MQ=255)
 ggTCAATTCGGCGAGGAGGTGATCTGCGGCTGAGTa                             <  1:6203065/36‑1 (MQ=255)
  gTCAATTCGGCGAGGCGGTGGTCTTCGGCTGAGTaa                            >  1:1611228/1‑36 (MQ=37)
  gTCAATTCGGCGAGGCGGTGATCTGCGGCTGGGTaa                            >  1:1460857/1‑36 (MQ=255)
  gTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTaa                            <  1:277866/36‑1 (MQ=255)
   tCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTaaa                           <  1:2902853/36‑1 (MQ=255)
   tCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTaaa                           <  1:2180511/36‑1 (MQ=255)
     gaTTCGGCGAGGCGGTGATCTGTTGCTGAGTTAAAt                         <  1:6793475/35‑1 (MQ=25)
     aaTTCGGCGAGGCGGTGATCTTCGGCTGAGTAAAAt                         >  1:7906047/1‑36 (MQ=255)
     aaTTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAAt                         >  1:87898/1‑36 (MQ=255)
     aaTTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAAt                         <  1:1600343/36‑1 (MQ=255)
     aaTTCGGCGAGGCGGAGATCTGCGGCTGGGTaaaaa                         >  1:1677184/1‑35 (MQ=37)
      aTTCGGCGAGGCGGTGATCTGCGGCTGGGTaaaaaa                        >  1:4829957/1‑34 (MQ=37)
       ttCGGCGAGGCGGGGATCTGCGGCTGGGTAAAATAc                       >  1:6590457/1‑36 (MQ=37)
        tCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATAcc                      <  1:2881348/36‑1 (MQ=255)
          ggCGAGGCGGTGGTCTGCGGGTGGGGGAAATACCGc                    >  1:2407319/1‑36 (MQ=16)
            ctgggCGGTGATCTGCGGCTGAGTAAAATACCGCCa                  <  1:6590637/33‑1 (MQ=255)
            cGAGGCGGTTATCTGCGGCTGAGAAAAATACCGCCa                  <  1:3591266/36‑1 (MQ=37)
            cGAGGCGGTGATCTTCGGCTGAGTAAAAAACCGCCa                  >  1:7458784/1‑36 (MQ=37)
            cGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCa                  <  1:2428633/36‑1 (MQ=255)
              aGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGt                >  1:6778726/1‑36 (MQ=255)
               ggCGGTGATCTGCGGCTGAGTAAAATACCGCCAGtt               >  1:1300181/1‑36 (MQ=255)
               ggCGGGGATCTGCGGCTGAGTAAAATACCGCCAGtt               <  1:5659600/36‑1 (MQ=255)
                  ggTGATCGGGGGCTGAGAAAAATACCGCCAGTTCAt            <  1:3115094/36‑1 (MQ=25)
                     taTCTGCGGCTGATAAAAATACCGCCAGTTCATTAt         <  1:2394421/35‑1 (MQ=37)
                     gATCTGCGGCTGAGTAAAATACCGCCAGTTCATTAt         >  1:1371469/1‑36 (MQ=255)
                     aaTCTGCGGATGAAAAAAAAACCGCCAGTTCATTAt         <  1:2459851/35‑1 (MQ=16)
                      aTCTGCGGCTGATAAAAATACCGCCAGTTCATTATc        <  1:7341697/36‑1 (MQ=37)
                       tcggCGGCTGAGAAAAATACCGCCAGTTCATTATCt       <  1:249569/33‑1 (MQ=37)
                       tcggCGGCTGAAAAAAATACCGCCAGTTCATTATCt       <  1:5492479/33‑1 (MQ=25)
                            ggCTGAGTAAAATACCGCCAGTTCATTATCTGATaa  >  1:2566503/1‑36 (MQ=255)
                                   |                            
TGGTCAATTCGGCGAGGCGGTGATCTGCGGCTGAGTAAAATACCGCCAGTTCATTATCTGATAA  >  REL606/452210‑452273

Base quality scores:  ATCG  < 3 ≤  ATCG  < 6 ≤  ATCG  < 11 ≤  ATCG  < 24 ≤  ATCG  < 37 ≤  ATCG