Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 5,101,324 G→A 7.8% G101G (GGC→GGT)  phhR ← sigma‑54 dependent transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029475,101,3240GA 7.8% 144.5 / 2.5 51G101G (GGC→GGT) phhRsigma‑54 dependent transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (24/23);  new base A (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

AAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGCCGCAGGGCCTGAAATT  >  NC_002947/5101178‑5101472
                                                                                                                                                  |                                                                                                                                                    
aaGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGAGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTgccgc                                                                                                                                                     <  6:258655/148‑1 (MQ=255)
aaGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGAGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTgccgc                                                                                                                                                     >  5:258655/1‑148 (MQ=255)
  gCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGACCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCACCCa                                                                                                                                                  >  8:333495/1‑149 (MQ=255)
         aTGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgat                                                                                                                                           >  5:41813/1‑149 (MQ=255)
          tGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgatc                                                                                                                                          >  7:175107/1‑149 (MQ=255)
           gcgcGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgatc                                                                                                                                          >  3:272780/1‑148 (MQ=255)
                  atgttgGCCCGCACCAACTCCGGAAGATCGAAGTCATCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCAc                                                                                                                                  <  8:119370/148‑1 (MQ=255)
                    gttgGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCg                                                                                                                                >  1:114491/1‑149 (MQ=255)
                     ttgGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCgg                                                                                                                               <  2:114491/149‑1 (MQ=255)
                       ggCCCGCACCAACTCCGGAAGATCGAAGACTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACACGCACGCCAAGCAACTGCGCGCCTGCACGGTTGGCCGCAACGATGCTGCCGCCCAAGTCGATCGACAGCACCggg                                                                                                                              >  1:133177/1‑148 (MQ=255)
                        gCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGaa                                                                                                                            <  7:298509/149‑1 (MQ=255)
                                     ccGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGccccc                                                                                                               >  2:208227/1‑149 (MQ=255)
                                      cGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGccccc                                                                                                               <  8:238259/148‑1 (MQ=255)
                                      cGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCa                                                                                                              >  7:261499/1‑149 (MQ=255)
                                            aTCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACg                                                                                                        >  6:155810/1‑149 (MQ=255)
                                                     ttctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgat                                                                                                                                           <  3:33509/105‑1 (MQ=255)
                                                     ttctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGtcgat                                                                                                                                           >  4:33509/1‑105 (MQ=255)
                                                     ttctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTc                                                                                                   >  5:196863/1‑145 (MQ=255)
                                                     ttctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTc                                                                                                   <  6:196863/145‑1 (MQ=255)
                                                     ttctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGACGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCACCGCCTTCAGCt                                                                                               >  8:324801/1‑149 (MQ=255)
                                                      tctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTc                                                                                              >  4:261550/1‑149 (MQ=255)
                                                       ctACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTc                                                                                              >  1:44595/1‑148 (MQ=255)
                                                               cgcgcCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCg                                                                                     <  2:232671/149‑1 (MQ=255)
                                                               cgcacCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCg                                                                                     >  4:205184/1‑149 (MQ=255)
                                                                gcgcCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCgg                                                                                    >  8:102597/1‑149 (MQ=255)
                                                                 cgcCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGc                                                                                   <  2:44595/149‑1 (MQ=255)
                                                                   ccAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGt                                                                                 <  6:41813/149‑1 (MQ=255)
                                                                       cGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGc                                                                             >  2:76229/1‑149 (MQ=255)
                                                                          cATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGGGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCATCGCATTCAGCTCCATGTGCCGGCGTTCGCTgg                                                                          <  2:133177/149‑1 (MQ=255)
                                                                          cATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTgg                                                                          <  1:75467/149‑1 (MQ=255)
                                                                               ccGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATc                                                                     <  3:261550/149‑1 (MQ=255)
                                                                               ccGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCACCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATc                                                                     <  7:333495/149‑1 (MQ=255)
                                                                                      cTCATCAACCCGCACGCCAAGCAACTGCGCGACTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGc                                                                 >  4:28790/1‑146 (MQ=255)
                                                                                      cTCATCAACCCGCACGCCAAGCAACTGCGCGACTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGc                                                                 <  3:28790/146‑1 (MQ=255)
                                                                                       tcatcaACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCca                                                              >  5:256532/1‑148 (MQ=255)
                                                                                         atcaACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCACCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGc                                                                 >  4:44478/1‑143 (MQ=255)
                                                                                         atcaACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCACCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGc                                                                 <  3:44478/143‑1 (MQ=255)
                                                                                            aaCCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGc                                                         <  8:175107/148‑1 (MQ=255)
                                                                                               ccGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTaa                                                     >  4:37432/1‑149 (MQ=255)
                                                                                                       cAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAAt                                             <  3:205184/149‑1 (MQ=255)
                                                                                                        aaGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATa                                            >  6:123764/1‑149 (MQ=255)
                                                                                                              cTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCgg                                      <  5:155810/149‑1 (MQ=255)
                                                                                                                   cgGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCATGCCCACACGCTTAACGCCGAATACCCCGGCAATg                                 <  7:102597/149‑1 (MQ=255)
                                                                                                                     gCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCa                                    >  2:234610/1‑144 (MQ=255)
                                                                                                                     gCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCa                                    <  1:234610/144‑1 (MQ=255)
                                                                                                                     gCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGc                               <  8:261499/149‑1 (MQ=255)
                                                                                                                         cACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTc                            <  4:272780/148‑1 (MQ=255)
                                                                                                                              ttGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACtt                      <  1:208227/149‑1 (MQ=255)
                                                                                                                                  ccGCAACGATGCTGCCGCCCATGTCGATCGACAGTACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGc                  >  5:138895/1‑149 (MQ=255)
                                                                                                                                  ccGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCg                                       >  2:95867/1‑128 (MQ=255)
                                                                                                                                  ccGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCg                                       <  1:95867/128‑1 (MQ=255)
                                                                                                                                   cGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGcc                 >  7:267288/1‑149 (MQ=255)
                                                                                                                                     cAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGGTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGACGAATACCCCGGCAATGGCCTCGAACTTCGGCCGc               <  5:123764/149‑1 (MQ=255)
                                                                                                                                               gccgccCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGCCGCAGGGCCTGa      >  6:131876/1‑148 (MQ=255)
                                                                                                                                                ccgccCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGCCGCAg             >  7:150459/1‑140 (MQ=255)
                                                                                                                                                ccgccCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGCCGCAg             <  8:150459/140‑1 (MQ=255)
                                                                                                                                                  gccCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGCCGCAGGGCCTGAAAtt  >  1:343703/1‑149 (MQ=255)
                                                                                                                                                  |                                                                                                                                                    
AAGCCGTTGATGCGCGACTTGTTGGCCCGCACCAACTCCGGAAGATCGAAGTCTTCTACGTAGCGCGCCAGCGGCATGCCCGGCACCTCATCAACCCGCACGCCAAGCAACTGCGCGGCTGCACGGTTGGCCGCAACGATGCTGCCGCCCATGTCGATCGACAGCACCGGGAAGTCCAGCGCCCCCAGCAACGCATTCAGCTCCATGTGCCGGCGTTCGCTGGGCATCAGGCCCACACGCTTAACGCCGAATACCCCGGCAATGGCCTCGAACTTCGGCCGCAGGGCCTGAAATT  >  NC_002947/5101178‑5101472

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: ‑