Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,969,310 C→T 9.1% intergenic (+259/‑56) PP_3498 → / → PP_3499 transposase/transposase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,969,3100CT 9.1% 149.9 / 5.0 55intergenic (+259/‑56)PP_3498/PP_3499transposase/transposase
Reads supporting (aligned to +/- strand):  ref base C (26/24);  new base T (2/3);  total (28/27)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.94e-01

GCCTCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTC  >  NC_002947/3969164‑3969410
                                                                                                                                                     |                                                                                                    
gCCTCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGa                                                                                                    <  2:15638/149‑1 (MQ=255)
gCCTCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGa                                                                                                    <  7:131754/149‑1 (MQ=255)
 ccTCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGATCTGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCg                                                                                                     <  1:271907/149‑1 (MQ=255)
  cTCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATg                                                                                                  <  7:299730/149‑1 (MQ=255)
   tCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCTATCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGTGAtc                                                                                                  >  1:263333/1‑148 (MQ=255)
      aTGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGgtgt                                                                                              >  8:106351/1‑149 (MQ=255)
      aTGTAAACGCCACACTGCGAACAAACAAAAATCTTTGCCACAAGCAAAAACCT‑TACTCGAATAGCCCTGATACATACA‑‑TGCAACCGCGATCCTAAGGTAAGAGTCCGACGAACTCACCTTCCGAACTCCAGCATTAACGTCAATGgtg                                                                                               >  4:44050/1‑148 (MQ=16)
           aaCGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcgcg                                                                                         >  8:108478/1‑149 (MQ=255)
           aaCGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCcgcg                                                                                         >  2:169237/1‑149 (MQ=255)
                   acTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGTGATCGCGTCCGCTTaaaaata                                                                                 >  6:192092/1‑143 (MQ=21)
                       cGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCg                                                                             >  6:226834/1‑149 (MQ=255)
                              accacGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGa                                                                      >  3:267263/1‑149 (MQ=255)
                                cacGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGAt                                                                     >  2:187653/1‑148 (MQ=255)
                                 acGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCa                                                                   >  3:151701/1‑149 (MQ=255)
                                  cGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAc                                                                  <  2:144250/149‑1 (MQ=255)
                                         ggCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTAt                                                            <  1:169237/148‑1 (MQ=255)
                                          gCCAGAATCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGTGATCGCGTCCGCTTAAAAATACGCGGACACCATCGCCCTTaat                                                           <  2:263333/148‑3 (MQ=21)
                                           ccAGAAGCAAATAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACGGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGc                                                         <  6:17514/149‑1 (MQ=255)
                                            cAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGTGATCGCGTCCGCTTAAAAATACGCGGACACCATCGCCCTTaatgct                                                        <  2:231069/149‑6 (MQ=21)
                                            cAGAAGCAAAAAGCT‑TCCTCCAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGTGATCGCGTCCGCTTAAAAATACGCGGACACCATCGCCCTTaatgct                                                        <  5:192092/149‑6 (MQ=21)
                                               aaGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAccc                                                                >  6:205862/1‑138 (MQ=255)
                                               aaGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCAccc                                                                <  5:205862/138‑1 (MQ=255)
                                                  cAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGAtt                                                  >  1:41619/1‑149 (MQ=255)
                                                   aaaaaGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGAtt                                                  <  4:267263/148‑1 (MQ=255)
                                                   aaaaaGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGAtt                                                  >  3:232585/1‑148 (MQ=255)
                                                    aaaaGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTc                                                <  7:263374/149‑1 (MQ=255)
                                                    aaaaGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTc                                                >  2:295482/1‑149 (MQ=255)
                                                     aaaGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCG‑CAGGAttt                                                 >  5:299190/1‑146 (MQ=255)
                                                     aaaGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCG‑CAGGAttt                                                 <  6:299190/146‑1 (MQ=255)
                                                         cT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGTTCACCCTTATCGCCAGGATTTCTATgc                                           <  1:187653/149‑1 (MQ=255)
                                                              cTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGAAAAAAGGGCGATGGTGTCCGAGCATTTTTAAGAGGAATCAATACCCGGTATCGCCAGGATTTCTATGCGcc                                        >  5:324807/1‑148 (MQ=18)
                                                               tCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCaa                                      >  7:39658/1‑149 (MQ=255)
                                                               tCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCAAGGATTTCTATGAGCCaa                                      >  8:165370/1‑149 (MQ=255)
                                                               tCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCaa                                      >  3:282384/1‑149 (MQ=255)
                                                                  aaTAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGa                                   <  2:41619/149‑1 (MQ=255)
                                                                      ggCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGct                               <  4:151701/149‑1 (MQ=255)
                                                                         cTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGACGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGGATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGctct                             >  8:123189/1‑148 (MQ=255)
                                                                          tGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGAttt                                                 <  8:265614/127‑1 (MQ=255)
                                                                          tGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGAttt                                                 >  7:265614/1‑127 (MQ=255)
                                                                            aTACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTa                           <  5:226834/147‑1 (MQ=255)
                                                                               cATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCg                       >  5:144560/1‑148 (MQ=255)
                                                                                aTAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGa                      >  5:21019/1‑148 (MQ=255)
                                                                                aTAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGa                      >  1:17424/1‑148 (MQ=255)
                                                                                 tAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaaa                    >  1:10898/1‑149 (MQ=255)
                                                                                       tGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCg                 <  7:106351/148‑1 (MQ=255)
                                                                                       tGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGt                <  7:108478/149‑1 (MQ=255)
                                                                                        gCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGt                >  2:42214/1‑148 (MQ=255)
                                                                                         cAACCGGTTTCCTATGGTATGCGTCCGGCGATCTGACGTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGtt               <  3:44050/148‑1 (MQ=14)
                                                                                           aCCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaa            <  6:198858/149‑1 (MQ=40)
                                                                                            ccGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaaa           <  3:134713/149‑1 (MQ=40)
                                                                                              gggTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGc         >  4:137748/1‑149 (MQ=38)
                                                                                                 ttCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCATCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGTACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCa      <  7:165370/149‑1 (MQ=25)
                                                                                                  tCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAg     >  2:297726/1‑149 (MQ=35)
                                                                                                    cTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaaa                    <  4:137435/132‑1 (MQ=33)
                                                                                                       tGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTc  <  1:295482/147‑1 (MQ=31)
                                                                                                                                                     |                                                                                                    
GCCTCAATGTAAACGGCACACTGCGAGCTCACCACGATGTTGGCCAGAAGCAAAAAGCT‑TCCTCGAATAGGCCTGATACATAGA‑‑TGCAACCGGGTTCCTATGGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTC  >  NC_002947/3969164‑3969410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑