Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,625,544 Δ1 bp 18.5% intergenic (‑57/+20) PP_3195 ← / ← PP_3196 hypothetical protein/nodulation protein d1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,625,5440T.18.5% 141.7 / 31.1 54intergenic (‑57/+20)PP_3195/PP_3196hypothetical protein/nodulation protein d1
Reads supporting (aligned to +/- strand):  ref base T (17/27);  new base . (8/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 3.23e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.17e-01

CTGCGGTCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCCACAGCATGA  >  NC_002947/3625396‑3625682
                                                                                                                                                    |                                                                                                                                           
cTGCGGTCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGgtgt                                                                                                                                             >  5:292915/1‑149 (MQ=255)
 tGCGGTCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTc                                                                                                                                            >  7:112233/1‑149 (MQ=255)
  gCGGTCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCt                                                                                                                                           >  8:116612/1‑149 (MQ=255)
   ccgccgcggAGCCCCGCCCCCACGGGAGCGCCCGGCCGGCAGGGCCCGGTTTGTAGTCAAGGTACGCAGGCAGGGCAGCGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCTCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTg                                                                                                                                          <  6:210846/142‑1 (MQ=255)
    ggTCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTgg                                                                                                                                         <  4:325124/149‑1 (MQ=255)
      tCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTgggg                                                                                                                                       <  6:250768/149‑1 (MQ=255)
      tCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTgggg                                                                                                                                       <  7:9608/149‑1 (MQ=255)
             gTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGgc                                                                                                                               >  4:321439/1‑149 (MQ=255)
                        agttGAGCGACAGGCAGCCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAgg                                                                                                                    <  3:361683/147‑1 (MQ=255)
                            gAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCgg                                                                                                                 <  6:292915/148‑1 (MQ=255)
                             aGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCggc                                                                                                                <  2:337178/148‑2 (MQ=255)
                              gCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGGGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCACTCAGGCGGTgg                                                                                                              <  5:182209/149‑1 (MQ=255)
                               cGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGgc                                                                                                             >  2:32625/1‑149 (MQ=255)
                                gACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGCGCAGGGTGGCGCCAATCGTGATCAGGGATCCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGCAGTCTGGGGCG‑CTGGCCCCCGCTCAGGCGGTGgcg                                                                                                            >  5:309311/1‑149 (MQ=255)
                                 aCAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGgcgc                                                                                                           >  4:147158/1‑149 (MQ=255)
                                    ggcaggcaggGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGCCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCa                                                                                                        <  1:32625/149‑1 (MQ=255)
                                      caggcaggGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCaga                                                                                                      <  2:272853/149‑1 (MQ=255)
                                                gcgGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCt                                                                                            <  5:56563/149‑1 (MQ=255)
                                                    tttGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGc                                                                                          <  4:134484/147‑1 (MQ=255)
                                                    tttGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGc                                                                                          >  3:134484/1‑147 (MQ=255)
                                                    tttGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGt                                                                                        >  7:18806/1‑149 (MQ=255)
                                                         aGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCGAATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTg                                                                                    <  1:278134/149‑1 (MQ=255)
                                                          ggCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGgc                                                                                  >  6:344385/1‑149 (MQ=255)
                                                              aGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCAc                                                                              >  3:26656/1‑149 (MQ=255)
                                                                gTACGCAGGCAGCGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTg                                                                            <  7:340278/149‑1 (MQ=255)
                                                                            ggcagggTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCt                                                                <  7:116612/149‑1 (MQ=255)
                                                                              caggtTGGGGGCAATCGTTTTCAGGGATGCGAGGTAGCGCGAAACGCGATGCCCCAGCACCGGTGCGGTGTCTGGGGCG‑ATGGCGGGCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCGGGCGCACTGAATGACATCGCTGa                                                              <  6:309311/149‑1 (MQ=255)
                                                                                           aTCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAg                                                 >  7:176745/1‑149 (MQ=255)
                                                                                              gTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGTGCACTGAATGACATCGCTGATGCGCTCGCGAAGcc                                               <  8:18806/148‑1 (MQ=255)
                                                                                                    aGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTca                                                      <  5:48670/135‑2 (MQ=255)
                                                                                                    aGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTca                                                      >  6:48670/1‑134 (MQ=255)
                                                                                                     gggATGCGAGGTATCGCGAAATGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGc                                       <  6:224136/149‑1 (MQ=255)
                                                                                                      ggATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCa                                      >  7:349088/1‑149 (MQ=255)
                                                                                                      ggATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGGGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCa                                      >  7:269293/1‑149 (MQ=255)
                                                                                                       gATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCAt                                     <  3:334593/149‑1 (MQ=255)
                                                                                                       gATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCAt                                     <  3:228125/149‑1 (MQ=255)
                                                                                                            gAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAAt                                                                         <  5:146862/108‑1 (MQ=255)
                                                                                                            gAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAAt                                                                         >  6:146862/1‑108 (MQ=255)
                                                                                                                    gcgAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTc                         >  8:176207/1‑148 (MQ=255)
                                                                                                                         aCGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAGGCCCTCTGTGCATGGGGTCGCCGTCCAtgct                   >  3:301818/1‑149 (MQ=255)
                                                                                                                            cgATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCg                <  3:321439/149‑1 (MQ=255)
                                                                                                                                 cccagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          >  8:35300/7‑149 (MQ=255)
                                                                                                                                 cccagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          >  5:299670/7‑149 (MQ=255)
                                                                                                                                 cccagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          >  3:165617/7‑149 (MQ=255)
                                                                                                                                  ccagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          >  6:382555/6‑148 (MQ=255)
                                                                                                                                  ccagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          >  2:372605/6‑148 (MQ=255)
                                                                                                                                  ccagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCCCTCAGGCGGTCGCGCGCACAGCATCTGGCTGCGTGCTGGCGCAATGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGCGGTCGCCGTCCATGCAGCGGTGAca          >  7:354738/6‑148 (MQ=255)
                                                                                                                                   ccAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCcac         <  3:147158/149‑1 (MQ=255)
                                                                                                                                   cagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          >  6:364228/5‑147 (MQ=255)
                                                                                                                                   cagacACCGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCca          <  5:364228/143‑1 (MQ=255)
                                                                                                                                      gCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCCACAGc      <  5:344385/149‑1 (MQ=255)
                                                                                                                                        aCCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCCACAGCAt    <  8:112233/149‑1 (MQ=255)
                                                                                                                                          cGCTGCTGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGTTGTCGCTAATATCATATGGCTTCGTGCTGGCGCACTGAATGACATCGCTGATGAGCTCGAGAAGCAATCTGTTCATGGGGTCTACTTCCATGCTGCGGTGCCACAGCATGa  <  6:366903/149‑1 (MQ=255)
                                                                                                                                          cGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTc                                                       <  2:96907/95‑1 (MQ=255)
                                                                                                                                          cGCAGCGGTG‑CTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTc                                                       >  1:96907/1‑95 (MQ=255)
                                                                                                                                                    |                                                                                                                                           
CTGCGGTCGTGGAGTCCGGCGCCCACTTGAGCGACAGGCAGGCAGGGCGCGGTTTGAAGGCAAGGTACGCAGGCAGGGCAGGGTGGGGCCAATCGTGATCAGGGATGCGAGGTATCGCGAAACGCGATGCCCCAGCACCGCTGCGGTGTCTGGGGCG‑ATGGCCGCCGCTCAGGCGGTGGCGCGCAGAGCATCTGGCTGCGTGCTGGCGCACTGAATGACATCGCTGATGCGCTCGCGAAGCCATCTGTGCATGGGGTCGCCGTCCATGCTGCGGTGCCACAGCATGA  >  NC_002947/3625396‑3625682

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑