Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,531,058 A→C 7.2% R421R (CGT→CGG)  braE ← high‑affinity branched‑chain amino acid ABC transporter permease BraE

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,531,0580AC 7.2% 154.2 / 2.5 54R421R (CGT→CGG) braEhigh‑affinity branched‑chain amino acid ABC transporter permease BraE
Reads supporting (aligned to +/- strand):  ref base A (23/27);  new base C (2/2);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CAAATATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACGGTCGAGCCCATGC  >  NC_002947/5530911‑5531206
                                                                                                                                                   |                                                                                                                                                    
cAAATATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACg                                                                                                                                                    >  2:768095/1‑150 (MQ=255)
 aaaTATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACgg                                                                                                                                                   >  2:224787/1‑150 (MQ=255)
   ctatCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGAt                                                                                                                                                 <  2:32373/149‑1 (MQ=255)
      tCTGGTTGCGCCGGACCTTCAGGCGGTCGGCGCGGAGCGCCTTGATGCCTCCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATCCGGATCAg                                                                                                                                              >  1:32373/1‑150 (MQ=255)
       cTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATCCGTATCAGc                                                                                                                                             <  2:341083/150‑1 (MQ=255)
            tGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCAcg                                                                                                                                        <  1:829080/150‑1 (MQ=255)
             gcgcCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCAcgc                                                                                                                                       <  2:591839/150‑1 (MQ=255)
             gcgcCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCAcgc                                                                                                                                       <  2:591630/150‑1 (MQ=255)
               gcCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCTCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGGTCAGCCCACGCgg                                                                                                                                     >  1:1181505/1‑150 (MQ=255)
                     ccTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGccc                                                                                                                               <  2:979051/150‑2 (MQ=255)
                       ttCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGcc                                                                                                                                            <  1:1212689/135‑1 (MQ=255)
                       ttCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGcc                                                                                                                                            >  2:1212689/1‑135 (MQ=255)
                       ttCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGa                                                                                                                             >  1:182160/1‑150 (MQ=255)
                              tGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatcat                                                                                                                      >  2:1229788/1‑150 (MQ=255)
                                aCGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGAtcatcatca                                                                                                                    <  1:1074050/150‑1 (MQ=255)
                                  gTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagc                                                                                                                  >  1:907298/1‑150 (MQ=255)
                                       tGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagcaccat                                                                                                             <  2:747295/150‑1 (MQ=255)
                                           cgcCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCa                                                                                                                                               <  2:876250/112‑1 (MQ=255)
                                           cgcCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCa                                                                                                                                               >  1:876250/1‑112 (MQ=255)
                                                      cACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAAcag                                                                                              >  2:1137877/1‑150 (MQ=255)
                                                       aCCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAAcagc                                                                                             >  1:770185/1‑150 (MQ=255)
                                                                 atcatcAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatc                                                                                                                        >  1:212623/1‑113 (MQ=255)
                                                                 atcatcAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGatcatc                                                                                                                        <  2:212623/113‑1 (MQ=255)
                                                                     tcaGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCTTCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTc                                                                               <  1:1356538/150‑1 (MQ=255)
                                                                      caGGTGGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCg                                                                              <  1:53429/150‑1 (MQ=255)
                                                                       aGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCgg                                                                             <  1:1137877/150‑1 (MQ=255)
                                                                              cGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATAc                                                                                                                                                     <  1:854438/71‑1 (MQ=255)
                                                                              cGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATAc                                                                                                                                                     >  2:854438/1‑71 (MQ=255)
                                                                                  cGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTgcgc                                                                  <  1:1229788/150‑1 (MQ=255)
                                                                                    agagaATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCgcag                                                                >  1:1049378/1‑150 (MQ=255)
                                                                                       gaATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagcaccatca                                                                                                           >  1:278698/1‑104 (MQ=255)
                                                                                       gaATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATcatcagcaccatca                                                                                                           <  2:278698/104‑1 (MQ=255)
                                                                                           gATATTGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTcc                                                         >  2:1248908/1‑150 (MQ=255)
                                                                                             tatCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCgg                                                       <  1:768095/150‑1 (MQ=255)
                                                                                              atCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGgc                                                      <  2:183630/150‑1 (MQ=255)
                                                                                               tcgtcgCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGgc                                                      >  1:427086/1‑149 (MQ=255)
                                                                                               tcgtcgCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGgc                                                      <  2:427086/149‑1 (MQ=255)
                                                                                                 gtcgCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGcc                                                   >  1:171539/1‑150 (MQ=255)
                                                                                                    gCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAAcagca                                                                                            >  1:393307/1‑106 (MQ=255)
                                                                                                    gCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAAcagca                                                                                            <  2:393307/106‑1 (MQ=255)
                                                                                                      tCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGc                                                                       >  2:323661/1‑125 (MQ=255)
                                                                                                      tCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGc                                                                       <  1:323661/125‑1 (MQ=255)
                                                                                                      tCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGt                                              <  2:171539/150‑1 (MQ=255)
                                                                                                           gcgcCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCa                                         <  2:1417970/150‑1 (MQ=255)
                                                                                                                    cTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAAcgccg                                >  2:1244422/1‑150 (MQ=255)
                                                                                                                     tttACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAAcgccgc                               >  2:745380/1‑150 (MQ=255)
                                                                                                                       tACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGa                             <  2:182160/150‑1 (MQ=255)
                                                                                                                          gTGGGGTCACACCGGTACGGCTAATACGGATCAGGCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCACCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGa                          >  2:521987/1‑150 (MQ=255)
                                                                                                                            ggggTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCCCGAACGCCGCGATGAcc                        <  2:770185/150‑1 (MQ=255)
                                                                                                                             gggTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCGCCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACca                       >  1:1352436/1‑150 (MQ=255)
                                                                                                                             gggTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACca                       <  2:907298/150‑1 (MQ=255)
                                                                                                                                         gtgggCTGATCCGTATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCa                 >  1:1253890/4‑144 (MQ=255)
                                                                                                                                         gtgggCTGATCCGTATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCa                 <  2:1253890/141‑1 (MQ=255)
                                                                                                                                                  tACGGATCAGCCCACGCGGTCGCCAGATCATCATCATCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACGGTCGAGCCCATGc  <  2:1181505/150‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                                    
CAAATATCTGGTTGCGCCGGACCTTCAGGCTGACGTCGCTGAGCGCCTTGATGCCACCGAACTGCATCATCAGGTTGTCGACCGAGAGAATGATATCGTCGCTCATGGCGCCACTCCTTTACGTGGGGTCACACCGGTACGGCTGATACGGATCAGCCCACGCGGTCGCCAGATCATCATCAGCACCATCAGCACGCCGAACAGCAGCACCCGGTACTCGGAGAAGCTGCGCAGCAGTTCCGGCGCCACGGTCAGCACGAACGCCGCGATGACCACACCCACGGTCGAGCCCATGC  >  NC_002947/5530911‑5531206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑