Predicted mutation
evidence seq id position mutation freq annotation gene description
RA REL606 3,045,956 C→A 26.9% L16F (TTG→TTT yghJ ← predicted inner membrane lipoprotein

Read alignment evidence...
  seq id position change freq score reads annotation genes product
*REL6063,045,9560C→A26.9% 10.3 ‑4.4 0.04048yghJpredicted inner membrane lipoprotein
Reads supporting (aligned to +/- strand):  new base (1/11):  ref base (15/13):  total (16/24)
Fisher's exact test strand distribution p-value = 1.22e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.00e+00

CCACCGCCATCACAACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAA  >  REL606/3045921‑3045991
                                   |                                   
ccACCGCCATCACAACCGGCTAACAGGGTTGCGCTc                                     <  1:4569869/36‑1 (MQ=255)
 cACCGCCATCACAACCGGCTAACAGGGTTGCGCTCa                                    <  1:6496342/36‑1 (MQ=255)
  aCCGCCATCACAACCGGCTAACAGGGTTGCGCTCaa                                   <  1:6997763/36‑1 (MQ=255)
  aCCGCCATCACAACCGGCTAACAGGGTTGCGCTCaa                                   >  1:4617794/1‑36 (MQ=255)
  aCCGCCATCACAACCGGCTAACAGGGTTGCGCTCaa                                   >  1:6150249/1‑36 (MQ=255)
    cGCCATCACACCCGGCTAACAGGGTTGCGCTCaaaa                                 <  1:709268/36‑1 (MQ=255)
    cGCCATCACAACCGGCTAACAGGGTTGCGCTCaaaa                                 <  1:6654749/36‑1 (MQ=255)
     gCCATCACAACCGGCTACCAGGGTTGCGCTCAAAAt                                <  1:2488313/36‑1 (MQ=255)
     gCCATCACAACCGGCTAACAGGGTTGCGCTCAAAAt                                >  1:7747281/1‑36 (MQ=255)
     gCCATCACAACCGGCTAACAGGGTTGCGCTCAAAAt                                >  1:534311/1‑36 (MQ=255)
     gCCATCACAACCGGCTAACAGGGTTGCGCTCAAAAt                                <  1:1584275/36‑1 (MQ=255)
        aTCACACCCGGCTAACATGGTTGCGCTCAAAATAGc                             <  1:6549989/36‑1 (MQ=38)
        aTCACAACCGGCTAACAGGGTTGCGCTCAAAATAGc                             >  1:5864537/1‑36 (MQ=255)
        aTCACAACCGGCTAACAGGGTTGCGCTCAAAATAGc                             <  1:5405109/36‑1 (MQ=255)
        aTCACAACCGGCTAACAGGGTTGCGCTCAAAATAGc                             >  1:4195072/1‑36 (MQ=255)
         tcgcaACCGGCTAACAGGGTTGCGCTCAAAATAGcc                            <  1:4070896/33‑1 (MQ=255)
          cacaACCGGCTAACAGGGTTGCGCTCAAAATAGCCg                           <  1:6927365/36‑1 (MQ=255)
          cacaACCGGCTAACAGGGTTGCGCTCAAAATAGCCg                           >  1:6340359/1‑36 (MQ=255)
              aCCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTaa                       >  1:3798461/1‑36 (MQ=255)
               ccGGCTAACAGGGTTGCGCTCAAAATAGCCGCTaaa                      <  1:6078116/36‑1 (MQ=255)
               ccGGCTAACAGGGTTGCGCTCAAAATAGCCGCTaaa                      >  1:6502202/1‑36 (MQ=255)
                cGGCTAACAGGGTTGCGCTAAAAATAGCCGCTaaaa                     <  1:2904003/36‑1 (MQ=255)
                 ggCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAg                    >  1:1860470/1‑36 (MQ=255)
                 ggCAAAAAGGTTTGCGATAAAAATAGCCGCTAAAAg                    <  1:3687282/36‑1 (MQ=12)
                  gcaaaCAGGTTTCCCCTAAAATTAGCCGCTAAAAGc                   <  1:2159587/33‑1 (MQ=12)
                  gCTAACAGGGTTGCGCTAAAAATAGCCGCTAAAAGc                   <  1:2260343/36‑1 (MQ=255)
                   caaaCAGGTTTGCGATAAAAATAGCCGCTAAAAGCg                  <  1:2291001/34‑1 (MQ=21)
                   cTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCg                  >  1:3365858/1‑36 (MQ=255)
                    tAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGa                 >  1:2891453/1‑36 (MQ=255)
                      aCAGGGTTGAACAAAAAATAGCCGCTAAAAGCGAtt               <  1:1438164/36‑1 (MQ=16)
                       cggggTTGCGATAAAAATAGCCGCTAAAAGCGAttt              <  1:3233007/34‑1 (MQ=25)
                       cAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGAttt              >  1:6738629/1‑36 (MQ=255)
                       cAGGGTTGCGCTAAAAATAGCCGCTAAAAGCGAttt              >  1:6675429/1‑36 (MQ=255)
                         gggTTGCGCTAAAAATAGCCGCTAAAAGCGATTTCt            <  1:7809724/36‑1 (MQ=255)
                          ggTTGCGATAAAAATAGCCGCTAAAAGCGATTTCtt           <  1:5796623/36‑1 (MQ=37)
                          ggTGGCGCAAAAAATAGCCGCTAAAAGCGATTTCtt           <  1:3247526/36‑1 (MQ=25)
                           tttGCGCTCAAAATAGCCGCTAAAAGCGATTTCTta          <  1:5095413/35‑1 (MQ=255)
                           gTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTta          >  1:531022/1‑36 (MQ=255)
                            ttGCGCTAAAAATAGCCGCTAAAAGCGATTTCTtat         <  1:6287049/36‑1 (MQ=255)
                             tGCGCTCAAAATAGCCGCTAAAAGCGATTTCTtata        >  1:259077/1‑36 (MQ=255)
                                ccTCAAAATAGCCGCTAAAAGCGATTTCTTATAttt     <  1:2694367/35‑1 (MQ=255)
                                   cAAAATAGCCGCTAAAAGCGATTTCTTATATTTaaa  >  1:5683821/1‑36 (MQ=255)
                                   cAAAATAGCCGCTAAAAGCGATTTCTTATATTTaaa  >  1:4825900/1‑36 (MQ=255)
                                   |                                   
CCACCGCCATCACAACCGGCTAACAGGGTTGCGCTCAAAATAGCCGCTAAAAGCGATTTCTTATATTTAAA  >  REL606/3045921‑3045991

Base quality scores:  ATCG  < 3 ≤  ATCG  < 7 ≤  ATCG  < 20 ≤  ATCG  < 30 ≤  ATCG  < 37 ≤  ATCG