Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,558,578 A→G 8.7% E104G (GAA→GGA)  rtcR → sigma 54‑dependent transcriptional regulator of rtcBA expression

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,558,5780AG 8.7% 140.7 / 4.2 46E104G (GAA→GGA) rtcRsigma 54‑dependent transcriptional regulator of rtcBA expression
Reads supporting (aligned to +/- strand):  ref base A (23/19);  new base G (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.16e-01

GAAACGCTTAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGA  >  NC_000913/3558436‑3558725
                                                                                                                                              |                                                                                                                                                   
gAAACGCTTAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAaaga                                                                                                                                               >  3:163500/1‑149 (MQ=255)
 aaaCGCTTAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAaagaa                                                                                                                                              <  1:436459/149‑1 (MQ=255)
 aaaCGCTTAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAaagaa                                                                                                                                              <  2:457931/149‑1 (MQ=255)
   aCGCTTAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGTATTTCGAAGAGGTCTACGCCTGACTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAagaaga                                                                                                                                            >  4:148431/1‑149 (MQ=255)
       ttAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTAt                                                                                                                                        <  1:2572/149‑1 (MQ=255)
               gATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTca                                                                                                                                <  4:323505/149‑1 (MQ=255)
               gATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTca                                                                                                                                >  1:72640/1‑149 (MQ=255)
                           gTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAAtt                                                                                                                                  <  1:177537/135‑1 (MQ=255)
                           gTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAAtt                                                                                                                                  >  2:177537/1‑135 (MQ=255)
                             ttCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTa                                                                                                                  <  4:163500/149‑1 (MQ=255)
                                gCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTAccc                                                                                                               <  3:318027/149‑1 (MQ=255)
                                   aGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACg                                                                                                            >  1:200424/1‑149 (MQ=255)
                                    gAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGt                                                                                                           >  4:437044/1‑149 (MQ=255)
                                      aaCAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTcg                                                                                                         >  2:148818/1‑149 (MQ=255)
                                                  gAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCt                                                                                             <  4:7444/149‑1 (MQ=255)
                                                    gCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTgg                                                                                           <  3:148431/149‑1 (MQ=255)
                                                         gagaTTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCGCATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTct                                                                                      <  2:117281/149‑1 (MQ=255)
                                                            aTTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTctgct                                                                                   >  2:343769/1‑149 (MQ=255)
                                                             ttGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTctgctg                                                                                  >  2:394682/1‑149 (MQ=255)
                                                                     cATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAgc                                                                          >  2:437698/1‑149 (MQ=255)
                                                                        aaCCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGcgcg                                                                       >  2:80591/1‑149 (MQ=255)
                                                                        aaCCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGcgcg                                                                       >  2:43874/1‑149 (MQ=255)
                                                                          cccATGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGtt                                                                     <  2:110781/149‑1 (MQ=255)
                                                                              tGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTaa                                                                                                                                    >  4:59342/1‑82 (MQ=255)
                                                                              tGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTaa                                                                                                                                    <  3:59342/82‑1 (MQ=255)
                                                                              tGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCt                                                                 >  3:35391/1‑149 (MQ=255)
                                                                              tGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTGTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCt                                                                 >  4:226224/1‑149 (MQ=255)
                                                                                 gATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTgcc                                                              <  2:91702/149‑1 (MQ=255)
                                                                                   tttCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTgcccg                                                            >  1:321591/1‑149 (MQ=255)
                                                                                   tttCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTgcccg                                                            >  4:69436/1‑149 (MQ=255)
                                                                                     tCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGGAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTgcccgcc                                                          >  1:327510/1‑149 (MQ=255)
                                                                                     tCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGGAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTgcccgcc                                                          >  1:330488/1‑149 (MQ=255)
                                                                                         agagGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGc                                                      <  4:95395/149‑1 (MQ=255)
                                                                                         agagGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGc                                                      >  3:95395/1‑149 (MQ=255)
                                                                                                 aCGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGGAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACaa                                              <  2:330488/149‑1 (MQ=255)
                                                                                                 aCGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGGAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACaa                                              <  2:327510/149‑1 (MQ=255)
                                                                                                   gcctgcctGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATc                                            >  3:115466/1‑149 (MQ=255)
                                                                                                    cctgcctgCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCt                                           >  3:231385/1‑149 (MQ=255)
                                                                                                        cctgcATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCAc                                       <  1:80591/149‑1 (MQ=255)
                                                                                                                         gTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGaa                      <  4:115466/149‑1 (MQ=255)
                                                                                                                         gTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGaa                      <  2:200424/149‑1 (MQ=255)
                                                                                                                           ggTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAGAAAGAACa                    <  3:437044/149‑1 (MQ=255)
                                                                                                                           ggTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACa                    <  1:437698/149‑1 (MQ=255)
                                                                                                                                 gAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCcgcg              >  3:256133/1‑149 (MQ=255)
                                                                                                                                          ccAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAgg     >  1:385948/1‑149 (MQ=255)
                                                                                                                                             gAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGa  >  2:455576/1‑149 (MQ=255)
                                                                                                                                              |                                                                                                                                                   
GAAACGCTTAAACGCGATATCGCCAGCGTTTCGCCAGAAACAGAAGTGGTGAGCGTTGAGATTGAACTGCATAACCCGTGGGATTTCGAAGAGGTCTACGCCTGCCTGCATGATTTCGCCCGTGGTTACGAGTTTCAGCCAGAAAAAGAAGACTATTTAATTCACATCACCACCGGTACCCACGTCGCGCAGATTTGCTGGTTTCTGCTGGCAGAAGCGCGTTACCTGCCCGCCCGGCTGATACAATCTTCACCTCCGCGCAAAAAAGAACAGCCGCGCGGCCCAGGTGA  >  NC_000913/3558436‑3558725

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑