Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,922,995 A→T 7.7% I88N (ATC→AAC)  PP_4332 ← chemotaxis protein CheW

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,922,9950AT 7.7% 151.8 / 2.6 52I88N (ATC→AAC) PP_4332chemotaxis protein CheW
Reads supporting (aligned to +/- strand):  ref base A (21/27);  new base T (2/2);  total (23/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.91e-01

GCCATTCTTGTTGCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCACCCGGTACCGGGGCAATCTCGGT  >  NC_002947/4922850‑4923140
                                                                                                                                                 |                                                                                                                                                 
gCCATTCTTGTTGCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCgatga                                                                                                                                                <  7:254096/149‑1 (MQ=255)
 ccATTCTTGTTGCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCgatgat                                                                                                                                               <  6:136597/149‑1 (MQ=255)
 ccATTCTTGTTGCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCgatgat                                                                                                                                               >  3:133703/1‑149 (MQ=255)
   aTTCTTGTTGCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGAtgatga                                                                                                                                             >  7:120578/1‑149 (MQ=255)
         gttgCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATa                                                                                                                                        <  2:626/148‑1 (MQ=255)
             cacaCGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTTGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGgt                                                                                                                                   <  3:85048/149‑1 (MQ=255)
             cacaCGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACggg                                                                                                                                    <  6:60630/148‑1 (MQ=255)
                  gCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGtgttgt                                                                                                                              <  2:268792/149‑1 (MQ=255)
                  gCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGtgttgt                                                                                                                              <  4:100089/149‑1 (MQ=255)
                    cTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCg                                                                                                                            <  8:8252/149‑1 (MQ=255)
                        aaggaaCTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCa                                                                                                                        <  6:266929/146‑1 (MQ=255)
                                 ggCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGTCTTCGATGATGACGATACGGGTGTTGTCGGTCACTtcggtc                                                                                                                <  4:3887/148‑1 (MQ=255)
                                   ccGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGc                                                                                                             <  8:120578/149‑1 (MQ=255)
                                          ttCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGc                                                                                                      >  2:167262/1‑149 (MQ=255)
                                          ttCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGc                                                                                                      >  1:82528/1‑149 (MQ=255)
                                                  ccACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGc                                                                                              >  4:341226/1‑149 (MQ=255)
                                                  ccACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGc                                                                                              <  2:82528/149‑1 (MQ=255)
                                                  ccACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGc                                                                                              <  4:173890/149‑1 (MQ=255)
                                                    aCGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGTTGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCt                                                                                             >  2:59952/1‑148 (MQ=255)
                                                    aCGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTg                                                                                            <  3:246860/149‑1 (MQ=255)
                                                     cGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGa                                                                                           <  1:167262/149‑1 (MQ=255)
                                                     cGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGa                                                                                           <  6:166634/149‑1 (MQ=255)
                                                         cGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGAcgc                                                                                        <  3:341226/148‑1 (MQ=255)
                                                           gcgcGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACgg                                                                                                                                     >  6:207468/1‑101 (MQ=255)
                                                           gcgcGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACgg                                                                                                                                     <  5:207468/101‑1 (MQ=255)
                                                           gcgcGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCa                                                                                                         >  6:143403/1‑129 (MQ=255)
                                                           gcgcGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCa                                                                                                         <  5:143403/129‑1 (MQ=255)
                                                            cgcgGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCgtgt                                                                                    <  2:120292/149‑1 (MQ=255)
                                                                gTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGTTGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGAt                                                                                >  2:207142/1‑149 (MQ=255)
                                                                gTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGAt                                                                                >  5:40662/1‑149 (MQ=255)
                                                                gTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGAt                                                                                <  3:241513/149‑1 (MQ=255)
                                                                   tCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGTCTTCGATGAAGACGAAACGGGAGTTGTCGGACACTTCGGTCGGAATCAGGCCAAAACGCTGACGCTTGTCCATCAc                                                                             >  5:217066/1‑149 (MQ=255)
                                                                    cGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAg                                                                                                        <  3:344964/121‑1 (MQ=255)
                                                                    cGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAg                                                                                                        >  4:344964/1‑121 (MQ=255)
                                                                      aTTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGTTGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGt                                                                          <  1:207142/149‑1 (MQ=255)
                                                                           ggACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACATCGGTAGGCATCAGGCCAAAACGCTGACGAGTGTCGATCACCGTcacca                                                                     >  5:60006/1‑149 (MQ=255)
                                                                           ggACTGGCGCAGGAAAACCACTACGGCCACGATGTAGAACAGAATGCCGACCACTTGCTTGTCGCCTTCGATGAAGACGATACGGGTGTTGTCGGACACTTCGGTCGGCATCAGGCCAAAACGCTCACTCGTGACGATCACCGTcacca                                                                     >  4:57058/1‑149 (MQ=255)
                                                                             aCTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACg                                                                   >  7:102133/1‑149 (MQ=255)
                                                                                 gcgcAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGTTGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTg                                                                <  1:59952/148‑1 (MQ=255)
                                                                                 gcgcAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGc                                                               >  7:165752/1‑149 (MQ=255)
                                                                                 gcgcAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGc                                                               >  7:276027/1‑149 (MQ=255)
                                                                                    cAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCcgc                                                            <  6:40662/149‑1 (MQ=255)
                                                                                      ggTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCTGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCagcg                                                           >  7:98217/1‑148 (MQ=255)
                                                                                       gTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCgcgc                                                          >  3:91098/1‑148 (MQ=255)
                                                                                             cACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCcgaattac                                                       >  1:311242/1‑139 (MQ=255)
                                                                                                      cACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCa                                          <  8:102133/149‑1 (MQ=255)
                                                                                                                aCCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCgtgt                                                                                    <  1:231040/97‑1 (MQ=255)
                                                                                                                aCCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCgtgt                                                                                    >  2:231040/1‑97 (MQ=255)
                                                                                                                   aGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCgg                             >  6:105154/1‑149 (MQ=255)
                                                                                                                    gAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCCCGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGgc                            >  4:90804/1‑149 (MQ=255)
                                                                                                                         ccGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCAcc                       <  4:133703/149‑1 (MQ=255)
                                                                                                                              cACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCACCCGGTa                  <  8:98217/149‑1 (MQ=255)
                                                                                                                                    cttgTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCACCCGGTACCggg             <  4:91098/148‑1 (MQ=255)
                                                                                                                                          ggCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCACCCGGTACCGGGGCAAtct      >  7:272296/1‑149 (MQ=255)
                                                                                                                                               cGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCACCCGGTACCGGGGCAATCTCGgt  <  5:105154/148‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                 
GCCATTCTTGTTGCACACGCCTTGAATGAACTTGGCCGACTCTTCGTTACCCACGTTCGGCGCGGTTTCGATTTCGGACTGGCGCAGGTAAACCACTTCGGCCACGCTGTCGACCAGAATGCCGACCACTTGCTTGTCGGCTTCGATGATGACGATACGGGTGTTGTCGGTCACTTCGGTCGGCATCAGGCCAAAACGCTGACGCGTGTCGATCACCGTCACCACGTTGCCGCGCAAGTTGATGATGCCCAGCACGTAGCTCGGCGCACCCGGTACCGGGGCAATCTCGGT  >  NC_002947/4922850‑4923140

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑