Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,578,676 C→T 7.7% S10S (AGC→AGT)  PP_5589 → rhs repeat‑associated core domain‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,578,6760CT 7.7% 147.5 / 2.4 52S10S (AGC→AGT) PP_5589rhs repeat‑associated core domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (23/25);  new base T (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.58e-01

CTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTCATCTGGCTCAT  >  NC_002947/3578534‑3578824
                                                                                                                                              |                                                                                                                                                    
cTATTTGGGGTGATGGCCATTGCTCCGTGTTTAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGttt                                                                                                                                                <  3:66532/149‑1 (MQ=255)
 tATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGtttt                                                                                                                                               >  5:85021/1‑149 (MQ=255)
   tttGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACTGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGttttt                                                                                                                                              <  3:247000/148‑1 (MQ=255)
   tttGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGttttt                                                                                                                                              <  4:152746/148‑1 (MQ=255)
       gggTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGaaa                                                                                                                                          <  6:85021/148‑1 (MQ=255)
         gTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGTCCGTTTTTGAAAggt                                                                                                                                       >  5:214899/1‑149 (MQ=255)
         gTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGTCCGTTTTTGAAAggt                                                                                                                                       >  1:19351/1‑149 (MQ=255)
         gTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGTCCGTTTTTGAAAggt                                                                                                                                       <  6:214899/149‑1 (MQ=255)
         gTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGTCCGTTTTTGAAAggt                                                                                                                                       <  2:19351/149‑1 (MQ=255)
                     gCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAg                                                                                                                            <  6:131344/148‑1 (MQ=255)
                            gtTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCt                                                                                                                     >  6:271936/1‑148 (MQ=255)
                             ttGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAggtggt                                                                                                                                    <  1:132994/132‑1 (MQ=255)
                             ttGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAggtggt                                                                                                                                    >  2:132994/1‑132 (MQ=255)
                                aaGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTg                                                                                                                >  3:88375/1‑149 (MQ=255)
                                       aTGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAggtg                                                                                                                                      <  5:27636/120‑1 (MQ=255)
                                       aTGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAggtg                                                                                                                                      >  6:27636/1‑120 (MQ=255)
                                           tGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATc                                                                                                     <  3:97143/149‑1 (MQ=255)
                                              tCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTg                                                                                                  >  8:73689/1‑149 (MQ=255)
                                                 tttAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTa                                                                                                >  5:145175/1‑148 (MQ=255)
                                                     gACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAAtt                                                                                            >  7:110997/1‑148 (MQ=255)
                                                              gTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCa                                                                                       <  8:110997/144‑1 (MQ=255)
                                                              gTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGAcc                                                                                   <  4:88375/148‑1 (MQ=255)
                                                              gTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGAcc                                                                                   >  5:161746/1‑148 (MQ=255)
                                                                    gggTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAgg                                                                            >  3:9487/1‑149 (MQ=255)
                                                                     ggTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAggg                                                                           <  5:271936/149‑1 (MQ=255)
                                                                       tATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAggg                                                                           >  8:135964/1‑147 (MQ=255)
                                                                           aTTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCa                                                                         >  1:45289/1‑145 (MQ=255)
                                                                           aTTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCa                                                                         <  2:45289/145‑1 (MQ=255)
                                                                               aGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCa                                                                                       >  2:18907/1‑127 (MQ=255)
                                                                               aGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCa                                                                                       <  1:18907/127‑1 (MQ=255)
                                                                               aGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGc                                                                          >  7:99187/1‑140 (MQ=255)
                                                                               aGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGc                                                                          <  8:99187/140‑1 (MQ=255)
                                                                                gtgttaggtaAACGAATGTATCAGCCAGCTTTTATGAGCTTCGCATCGCCGGAGGCCGTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCaga                                                                <  4:53410/145‑1 (MQ=255)
                                                                                    taggtaAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCg                                                            <  7:73689/149‑1 (MQ=255)
                                                                                              aTTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAg                                                  >  4:95491/1‑149 (MQ=255)
                                                                                               ttGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAg                                                  >  5:273293/1‑148 (MQ=255)
                                                                                                  tATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAg                                              <  3:95491/149‑1 (MQ=255)
                                                                                                   aTCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAg                                              >  3:68125/1‑148 (MQ=255)
                                                                                                      tGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGaaa                                           >  4:248748/1‑148 (MQ=255)
                                                                                                         cAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAg                                                      >  5:238929/1‑134 (MQ=255)
                                                                                                         cAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAg                                                      <  6:238929/134‑1 (MQ=255)
                                                                                                          aGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAatcat                                      <  3:248748/149‑1 (MQ=255)
                                                                                                          aGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTAATCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAatcat                                      <  6:145175/149‑1 (MQ=255)
                                                                                                           gCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAatcat                                      >  7:250418/1‑148 (MQ=255)
                                                                                                            cTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAAtcatca                                    <  5:161315/149‑1 (MQ=255)
                                                                                                              ttGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAAtcatca                                    >  3:253966/1‑147 (MQ=255)
                                                                                                                   gcgcTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCAAGAGTCGCCGAAGCTAGTAAGAAAATCATCacagacag                             >  7:11854/1‑149 (MQ=255)
                                                                                                                          gCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTc                      <  4:9487/149‑1 (MQ=255)
                                                                                                                               gCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGaaa                  <  1:163924/148‑1 (MQ=255)
                                                                                                                               gCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGaaa                  <  4:68125/148‑1 (MQ=255)
                                                                                                                                        cTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCATACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTCATCTg        >  2:171332/1‑149 (MQ=255)
                                                                                                                                           gAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTCATCTGGc      <  8:250418/148‑1 (MQ=255)
                                                                                                                                              cccGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCATGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTCATCTGGCTCAt  <  6:161746/149‑1 (MQ=255)
                                                                                                                                              cccGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTc             >  6:152228/1‑138 (MQ=255)
                                                                                                                                              cccGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTc             <  5:152228/138‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                                    
CTATTTGGGGTGATGGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAGGCCCCAGAGTCGCCGAAGCTAGTAAGAAAATCATCACAGACAGCCCCGTCGAAACCCTCATCTGGCTCAT  >  NC_002947/3578534‑3578824

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: ‑