Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,229,085 G→C 7.6% E753D (GAG→GAC)  PP_1072 → leucine‑rich repeat‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,229,0850GC 7.6% 163.8 / 5.2 53E753D (GAG→GAC) PP_1072leucine‑rich repeat‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (29/20);  new base C (2/2);  total (31/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

CCTGCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCTGTCAGTCCAG  >  NC_002947/1228944‑1229233
                                                                                                                                             |                                                                                                                                                    
gctccggcgTCGCGCCAATCCGGGCACCGAACGCCTGGCTTTGGGCTGGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGACTCTgcgcc                                                                                                                                              <  2:275676/144‑2 (MQ=255)
 cTGCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAg                                                                                                                                             <  2:512618/150‑1 (MQ=255)
   gCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCGCAGTCTGCGCAGGa                                                                                                                                           >  2:65942/1‑150 (MQ=255)
           gCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGgt                                                                                                                                   <  1:376916/150‑1 (MQ=255)
             gTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGgtgt                                                                                                                                 >  1:430673/1‑150 (MQ=255)
               cAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTAt                                                                                                                               >  1:701458/1‑150 (MQ=255)
                   ccGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTg                                                                                                                           <  2:1148507/150‑1 (MQ=255)
                      gACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTgcgc                                                                                                                        >  2:789349/1‑150 (MQ=255)
                           cGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTgc                                                                                                                          <  1:1106074/143‑1 (MQ=255)
                           cGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTgc                                                                                                                          >  2:1106074/1‑143 (MQ=255)
                            gAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCgcggc                                                                                                                  <  2:697326/150‑1 (MQ=255)
                                      cTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATc                                                                                                        >  1:464632/1‑150 (MQ=255)
                                       tttGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCg                                                                                                       >  2:370564/1‑150 (MQ=255)
                                       tttGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCAGTGGCGACGGCTATCg                                                                                                       >  2:1098112/1‑150 (MQ=255)
                                                 cTCGAGCGTCAGCTGAAAGGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGt                                                                                             <  2:531166/150‑1 (MQ=255)
                                                           aGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCCCTACGCCGGTCAAGGTACAt                                                                                   >  2:220507/1‑150 (MQ=255)
                                                                 aaTGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGcc                                                                             <  2:701458/150‑1 (MQ=255)
                                                                     gCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTa                                                                         >  2:305186/1‑150 (MQ=255)
                                                                             cccTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCTGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTggcgg                                                                 <  1:1055165/150‑1 (MQ=255)
                                                                              ccTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTggcggc                                                                >  2:856569/1‑150 (MQ=255)
                                                                               cTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTAc                                                                                                                                      >  1:1181946/1‑79 (MQ=255)
                                                                               cTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTAc                                                                                                                                      <  2:1181946/79‑1 (MQ=255)
                                                                                   gcATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGt                                                           <  1:370564/150‑1 (MQ=255)
                                                                                     aTCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTg                                                         >  2:936231/1‑150 (MQ=255)
                                                                                     aTCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTg                                                         >  1:374006/1‑150 (MQ=255)
                                                                                       cGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGc                                                       >  1:819258/1‑150 (MQ=255)
                                                                                        gAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCt                                                      >  2:255526/1‑150 (MQ=255)
                                                                                               gcgAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTgg                                               >  2:563969/1‑150 (MQ=255)
                                                                                                cgAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGa                                              <  1:936231/150‑1 (MQ=255)
                                                                                                 gAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCAATGTTGGCTGCGCTGGAc                                             <  1:1189816/150‑1 (MQ=255)
                                                                                                     gTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACgg                                                                                                                                    <  2:198772/59‑1 (MQ=255)
                                                                                                     gTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACgg                                                                                                                                    >  1:198772/1‑59 (MQ=255)
                                                                                                           cGAGTGGCCGTTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGa                                   >  2:505239/1‑150 (MQ=255)
                                                                                                               tggccggtatctggccggtatcGGCGCAGAGTCTGCGCAgg                                                                                                                                            >  1:521225/1‑41 (MQ=255)
                                                                                                               tggccggtatctggccggtatcGGCGCAGAGTCTGCGCAgg                                                                                                                                            <  2:521225/41‑1 (MQ=255)
                                                                                                               tggccggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGc                               <  1:789349/150‑1 (MQ=255)
                                                                                                               tggccggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGc                               <  2:430673/150‑1 (MQ=255)
                                                                                                                   cggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGAt                           >  2:2859/1‑150 (MQ=255)
                                                                                                                   cggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGATGGCCGAGAAACAGACAGCCGac                           >  2:670583/1‑149 (MQ=255)
                                                                                                                          tggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAgg                                                                                        >  1:708162/1‑82 (MQ=255)
                                                                                                                          tggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAgg                                                                                        <  2:708162/82‑1 (MQ=255)
                                                                                                                          tggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCg                    >  1:672661/1‑150 (MQ=255)
                                                                                                                            gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGAt                  >  2:1159931/1‑150 (MQ=255)
                                                                                                                            gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGAt                  >  2:176080/1‑150 (MQ=255)
                                                                                                                                gtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACAt                                                                                   <  1:1039623/81‑1 (MQ=255)
                                                                                                                                gtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACAt                                                                                   >  2:1039623/1‑81 (MQ=255)
                                                                                                                                gtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCg              >  2:355126/1‑150 (MQ=255)
                                                                                                                                  atcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCt            <  1:563969/150‑1 (MQ=255)
                                                                                                                                   cctgcgcAGACTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCTg           >  1:964376/4‑150 (MQ=255)
                                                                                                                                      gcgcAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAg                                >  1:966752/1‑126 (MQ=255)
                                                                                                                                      gcgcAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAg                                <  2:966752/126‑1 (MQ=255)
                                                                                                                                      gcgcAGACTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGa                                              >  1:923778/1‑112 (MQ=255)
                                                                                                                                      gcgcAGACTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGa                                              <  2:923778/112‑1 (MQ=255)
                                                                                                                                            agTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCTGTCAGTCCAg  <  1:176080/150‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                                    
CCTGCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCTGTCAGTCCAG  >  NC_002947/1228944‑1229233

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑