Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,306,249 C→T 8.3% V194M (GTG→ATG)  PP_2907 ← two‑component system response regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,306,2490CT 8.3% 132.0 / 2.2 48V194M (GTG→ATG) PP_2907two‑component system response regulator
Reads supporting (aligned to +/- strand):  ref base C (18/26);  new base T (2/2);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCGCCAGCAGGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAGGGTGTTGTCACCGCG  >  NC_002947/3306112‑3306396
                                                                                                                                         |                                                                                                                                                   
aGCGCCAGCAGGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGt                                                                                                                                          >  3:187402/1‑149 (MQ=255)
 gcgcCAGCAGGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGTCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGtt                                                                                                                                         <  8:270619/149‑1 (MQ=255)
  cgcCAGCAGGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTg                                                                                                                                        <  6:103467/149‑1 (MQ=255)
   gcCAGCAGGCGGCTGGTAGAAGAACTCCCGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTgg                                                                                                                                       >  6:225927/1‑149 (MQ=255)
     cagcagGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTg                                                                                                                                     <  5:172616/149‑1 (MQ=255)
         cggcggcTGGTAGACCAACTCCTGCCTTTAGCCGGTTTCAGCACTGGCAAAGCCGGAGCCCCGTACCGTACTGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCg                                                                                                                                 <  2:339596/148‑1 (MQ=255)
         agGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCg                                                                                                                                 <  1:309324/149‑1 (MQ=255)
         agGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCg                                                                                                                                 <  4:213134/149‑1 (MQ=255)
                tGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGCGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCg                                                                                                                            >  5:376500/1‑147 (MQ=255)
                  gTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCATGTCGATCAGGTTGGTGCCCGGATCGAAGt                                                                                                                        >  8:212198/1‑149 (MQ=255)
                  gTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCATGTCGATCAGGTTGGTGCCCGGATCGAAGt                                                                                                                        >  8:206660/1‑149 (MQ=255)
                  gTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGt                                                                                                                        <  7:81431/149‑1 (MQ=255)
                       agaaCTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAg                                                                                                                   <  4:50850/149‑1 (MQ=255)
                          aCTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGccc                                                                                                                <  2:207266/149‑1 (MQ=255)
                           cTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCGCCGTAGCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGTCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGcccc                                                                                                               <  2:324558/149‑1 (MQ=255)
                            tCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGaa                                                                                                                          <  3:352085/137‑1 (MQ=255)
                            tCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGaa                                                                                                                          >  4:352085/1‑137 (MQ=255)
                              cacccTTTACTCGGGTTCAGCCATGGCATAGCCGGAGCCCCGTACCGTACGGTTCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGCTTGGTGCCCGGATCGAAGTGATAGCCCCAGa                                                                                                            <  6:342194/146‑1 (MQ=255)
                                     tAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTcc                                                                                                       <  7:266269/147‑1 (MQ=255)
                                     tAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCt                                                                                                      <  3:1395/148‑1 (MQ=255)
                                            gTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAatc                                                                                              <  2:239498/149‑1 (MQ=255)
                                            gTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAatc                                                                                              <  5:137161/149‑1 (MQ=255)
                                             ttCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAatca                                                                                             >  1:3962/1‑149 (MQ=255)
                                                aGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGGACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAatcatca                                                                                          <  7:115748/149‑1 (MQ=255)
                                                aGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAatcatc                                                                                           <  5:212573/148‑1 (MQ=255)
                                                        cATAGCCGGAGCCCCGTACGGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCTGACTTCCTCGAAAATCATCATCCGCGTg                                                                                  <  4:187402/149‑1 (MQ=255)
                                                                     ccgtaccgtaCGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGc                                                                     >  2:321373/1‑149 (MQ=255)
                                                                     cagtaccgtacGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCg                                                                      >  8:27490/3‑148 (MQ=255)
                                                                           cgtacGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCTTCATCCGCGTGATCACCTGGCCGCTGTGgc                                                               <  5:225927/149‑1 (MQ=255)
                                                                             tacGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCtgtg                                                                 >  7:47651/1‑145 (MQ=255)
                                                                             tacGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCtgtg                                                                 <  8:47651/145‑1 (MQ=255)
                                                                                  aTCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGGTCACCTGGCCGCTGTGGCGCATCAg                                                        >  7:31807/1‑149 (MQ=255)
                                                                                   tCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAgg                                                       >  1:300967/1‑149 (MQ=255)
                                                                                        ggcgACTGGCCGGGTGAGTCGATCTTCTTGCTCAGGCGGCCGATGTTCATGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTc                                                  <  7:206660/149‑1 (MQ=255)
                                                                                        ggcgACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCATGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTc                                                  <  7:212198/149‑1 (MQ=255)
                                                                                         gcgACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTAcac                                                  >  4:199898/1‑146 (MQ=255)
                                                                                           gACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCcag                                               <  3:199898/149‑1 (MQ=255)
                                                                                                gCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCACCAGCt                                          >  8:287167/1‑149 (MQ=255)
                                                                                                gCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATAATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCt                                          >  1:103436/1‑149 (MQ=255)
                                                                                                                  cttGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTggg                             <  1:321373/144‑1 (MQ=255)
                                                                                                                     gcgcAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAgg                      <  2:3962/148‑1 (MQ=255)
                                                                                                                       gcAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCAGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGtt                    >  6:149695/1‑148 (MQ=255)
                                                                                                                        cAGGCGGCCGATGTCCACGTCGATCAGGTTGGTGCCCGGAGCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGAGCACCTGGCCGCTGTGGCGCATCAGTTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGa                  <  8:296295/149‑1 (MQ=255)
                                                                                                                          ggcggcCGAAGTGCACCGCGATCCGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAgg                <  2:203430/149‑1 (MQ=255)
                                                                                                                                    gtgCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAGGGTGTTGTCAc      >  6:275271/1‑149 (MQ=255)
                                                                                                                                      gCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAGGGTGTTGTCACcg    >  6:236294/1‑149 (MQ=255)
                                                                                                                                       cACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAGGGTGTTGTCACcgc   >  3:177967/1‑149 (MQ=255)
                                                                                                                                        aCGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAGGGTGTTGTCACcgcg  >  6:275706/1‑149 (MQ=255)
                                                                                                                                         |                                                                                                                                                   
AGCGCCAGCAGGCGGCTGGTAGAAGAACTCCAGCCTTTAGACGGGTTCAGCAATGGCATAGCCGGAGCCCCGTACCGTACGGATCAGCGGCGACTGGCCGGGTGAGTCGATCTTCTTGCGCAGGCGGCCGATGTGCACGTCGATCAGGTTGGTGCCCGGATCGAAGTGATAGCCCCAGACTTCCTCGAAAATCATCATCCGCGTGATCACCTGGCCGCTGTGGCGCATCAGGTACTCCAGCAGCTTGTACTCGGTGGGCAACAGGTTGAGGGTGTTGTCACCGCG  >  NC_002947/3306112‑3306396

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑