Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 4,100,839 C→T 8.3% A238V (GCG→GTG)  PP_3608 → LysR family transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,100,8390CT 8.3% 132.9 / 2.2 50A238V (GCG→GTG) PP_3608LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (22/22);  new base T (2/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

AGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTGGCACAACC  >  NC_002947/4100694‑4100985
                                                                                                                                                 |                                                                                                                                                   
aGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCgg                                                                                                                                                   >  3:122695/1‑148 (MQ=255)
            gCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCGCACTCCAGTGTGGCaa                                                                                                                                                <  1:271537/139‑2 (MQ=255)
            gCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCGCACTCCAGTGTGGCaa                                                                                                                                                >  2:271537/1‑138 (MQ=255)
                     gACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCAc                                                                                                                             >  2:178748/1‑149 (MQ=255)
                                           tATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGcc                                                                                                      <  4:122695/149‑1 (MQ=255)
                                                     cATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCa                                                                                                                              >  6:74933/1‑116 (MQ=255)
                                                     cATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCa                                                                                                                              <  5:74933/116‑1 (MQ=255)
                                                         cgcCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTggg                                                                                        <  7:83182/149‑1 (MQ=255)
                                                          gcCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGAc                                                                                                                         >  6:221251/1‑116 (MQ=255)
                                                          gcCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGAc                                                                                                                         <  5:221251/116‑1 (MQ=255)
                                                            ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                                    >  3:3957/1‑103 (MQ=255)
                                                            ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                                    >  3:8814/1‑103 (MQ=255)
                                                            ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                                    <  4:3957/103‑1 (MQ=255)
                                                            ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                                    <  4:8814/103‑1 (MQ=255)
                                                             cGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCg                                                                                    <  3:278549/149‑1 (MQ=255)
                                                               gATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGtt                                                                                  >  1:277776/1‑149 (MQ=255)
                                                               gATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGtt                                                                                  <  1:178748/149‑1 (MQ=255)
                                                                    tttCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGACCAGCCGCGCTGTGGGGTCGTTgcgc                                                                              >  1:227584/1‑148 (MQ=255)
                                                                         aTGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAaca                                                                         >  8:69627/1‑148 (MQ=255)
                                                                         aTGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAaca                                                                         >  5:309033/1‑148 (MQ=255)
                                                                          tGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGAcc                                                                                                                        <  6:117375/101‑1 (MQ=255)
                                                                           gAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAac                                                                          >  4:17952/1‑145 (MQ=255)
                                                                           gAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAac                                                                          <  3:17952/145‑1 (MQ=255)
                                                                            aaaTCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACaa                                                                      <  7:69627/148‑1 (MQ=255)
                                                                                 gAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACt                                                                >  8:25251/1‑149 (MQ=255)
                                                                                  cgttgtcACTGGCCGCCCGGGGGTTGCAGCGCCGTATTGGCCTGGGCTTGGCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAGTTGGCGAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGacac                                                                 <  1:243925/142‑1 (MQ=255)
                                                                                   gCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTgc                                                              <  2:277776/149‑1 (MQ=255)
                                                                                     gTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTgcgc                                                            >  3:298723/1‑149 (MQ=255)
                                                                                        cACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGACCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAg                                                         <  2:227584/149‑1 (MQ=255)
                                                                                         aCTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGt                                                        >  3:215885/1‑149 (MQ=255)
                                                                                         aCTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGAGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGAGCCAACACAAGACACtacatcgg                                                         >  2:243925/1‑141 (MQ=255)
                                                                                         aCTGGCCGACCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGt                                                        >  6:204/1‑149 (MQ=255)
                                                                                           tGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCt                                                                                                                 >  8:71948/1‑91 (MQ=255)
                                                                                           tGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCt                                                                                                                 <  7:71948/91‑1 (MQ=255)
                                                                                                           gCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCa                                      >  3:134654/1‑149 (MQ=255)
                                                                                                                    tATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGt                             >  4:187500/1‑149 (MQ=255)
                                                                                                                      ttGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TCGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGGCACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTc                           >  5:304593/1‑149 (MQ=255)
                                                                                                                      ctGCCCGGCCCTTGCCCCTCTGGCGTGGGGCAGTCGAAGTGCTGGCCGGCACCGAGCTGATCCTGACAG‑TGGCCAGCCGCGCTGGGGGTTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTc                           <  4:36918/148‑1 (MQ=255)
                                                                                                                         cccTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACt                                           <  6:19980/130‑1 (MQ=255)
                                                                                                                         cccTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACt                                           >  5:19980/1‑130 (MQ=255)
                                                                                                                         cccTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGa                         <  6:309033/148‑1 (MQ=255)
                                                                                                                           cTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTa                      >  4:327287/1‑149 (MQ=255)
                                                                                                                              gCCTTGCCACTCTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATc                    <  6:304593/148‑1 (MQ=255)
                                                                                                                              gCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATc                    <  4:215885/148‑1 (MQ=255)
                                                                                                                                 ttGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGCCCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGc                 >  5:67760/1‑148 (MQ=255)
                                                                                                                                   gCCGCACTCCAGTGTGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTgg                                         >  7:296903/1‑122 (MQ=255)
                                                                                                                                   gCCGCACTCCAGTGTGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTgg                                         <  8:296903/122‑1 (MQ=255)
                                                                                                                                   gCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCaa               <  5:204/148‑1 (MQ=255)
                                                                                                                                       cacTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTg          <  7:25251/149‑1 (MQ=255)
                                                                                                                                               tGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCAAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTGGCACAAcc  <  3:187500/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                   
AGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTGGCACAACC  >  NC_002947/4100694‑4100985

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: ‑