Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,229,079 G→C 9.3% 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_0029471,229,0790GC 9.3% 164.7 / 7.5 54E753D (GAG→GAC) PP_1072leucine‑rich repeat‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (22/27);  new base C (2/3);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.27e-01

GCGCCTGCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCT  >  NC_002947/1228935‑1229217
                                                                                                                                                |                                                                                                                                          
gcgcCTGCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTg                                                                                                                                        >  3:125462/1‑149 (MQ=255)
       ccGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGACTCTgcgccga                                                                                                                                  <  3:259433/148‑4 (MQ=255)
       ccGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGACTCTgcgccga                                                                                                                                  <  4:144247/148‑4 (MQ=255)
              gCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACg                                                                                                                           <  4:138053/148‑1 (MQ=255)
                gTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGgtg                                                                                                                        <  7:204758/149‑1 (MQ=255)
                    aTCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATc                                                                                                                    >  4:109477/1‑149 (MQ=255)
                       cGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTg                                                                                                                 <  3:305330/149‑1 (MQ=255)
                        ggACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTgc                                                                                                                >  7:166307/1‑149 (MQ=255)
                            acCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGcgccg                                                                                                            >  5:142920/1‑149 (MQ=255)
                              cGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCcgcg                                                                                                          >  4:126508/1‑149 (MQ=255)
                              agAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCACGATGTACGGTGTATCGTTAGCcgcg                                                                                                          >  2:332367/2‑149 (MQ=255)
                                    ccTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACg                                                                                                    >  2:343927/1‑149 (MQ=255)
                                     cTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCATAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACgg                                                                                                   >  3:175885/1‑149 (MQ=255)
                                     cTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACgg                                                                                                   >  3:230784/1‑149 (MQ=255)
                                           ttGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATc                                                                                              <  4:175885/148‑1 (MQ=255)
                                                 ttGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGc                                                                                       >  8:48252/1‑149 (MQ=255)
                                                   gCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGc                                                                                       <  1:343927/147‑1 (MQ=255)
                                                    cTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCATGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCgg                                                                                    <  1:332367/149‑1 (MQ=255)
                                                     tCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGa                                                                                                                                 <  4:258279/103‑1 (MQ=255)
                                                        aGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAgg                                                                                                                                  >  6:56416/1‑99 (MQ=255)
                                                        aGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAgg                                                                                                                                  <  5:56416/99‑1 (MQ=255)
                                                          cGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAgg                                                                              <  4:230784/149‑1 (MQ=255)
                                                               gCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACAt                                                                         <  2:320554/149‑1 (MQ=255)
                                                                   aaaTGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTAc                                                                                                                            <  2:130995/94‑1 (MQ=255)
                                                                   aaaTGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTAc                                                                                                                            >  1:130995/1‑94 (MQ=255)
                                                                        gCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGcccc                                                                 >  6:181904/1‑148 (MQ=255)
                                                                         ccGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTa                                                               <  7:48252/149‑1 (MQ=255)
                                                                          cGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTAc                                                              <  3:126508/149‑1 (MQ=255)
                                                                                 ccTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCa                                                                                                                                    <  8:92683/72‑1 (MQ=255)
                                                                                 ccTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCa                                                                                                                                    >  7:92683/1‑72 (MQ=255)
                                                                                  cTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTggcgg                                                       >  4:326048/1‑148 (MQ=255)
                                                                                           gAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGc                                             >  2:80064/1‑149 (MQ=255)
                                                                                           gAACTGCGCGAAGGTAGCCCGAGGGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGc                                             <  3:165977/149‑1 (MQ=255)
                                                                                              cTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACgg                                                                                                                          >  6:220393/1‑69 (MQ=255)
                                                                                              cTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACgg                                                                                                                          <  5:220393/69‑1 (MQ=255)
                                                                                                 cgcgAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCt                                       <  3:128375/149‑1 (MQ=255)
                                                                                                 cgcgAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCt                                       >  4:6450/1‑149 (MQ=255)
                                                                                                    gAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGa                                    <  6:142920/149‑1 (MQ=255)
                                                                                                         tAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACgaga                               <  5:46614/149‑1 (MQ=255)
                                                                                                                   ggccggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGc                     <  3:6450/149‑1 (MQ=255)
                                                                                                                    gccggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGcc                    <  8:166307/149‑1 (MQ=255)
                                                                                                                     ccggtatctggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCg                   <  1:80064/149‑1 (MQ=255)
                                                                                                                             tggccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGGCGAGACGCAGACAGCCGCTCTCGGc           >  8:287532/1‑149 (MQ=255)
                                                                                                                               gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTgg                                              <  1:150567/112‑1 (MQ=255)
                                                                                                                               gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTgg                                              >  2:150567/1‑112 (MQ=255)
                                                                                                                               gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCgg            <  3:109477/146‑1 (MQ=255)
                                                                                                                               gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCgg            <  8:23214/146‑1 (MQ=255)
                                                                                                                               gccggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGa         <  3:326048/149‑1 (MQ=255)
                                                                                                                                 cggtatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTGGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATg       >  5:295362/1‑149 (MQ=255)
                                                                                                                                    tatcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCg    <  5:181904/149‑1 (MQ=255)
                                                                                                                                     tcctgcgcAGACTCTGCGCCGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCt                                       >  5:272133/5‑113 (MQ=255)
                                                                                                                                     tcctgcgcAGACTCTGCGCCGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCt                                       <  6:272133/109‑1 (MQ=255)
                                                                                                                                      tcGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATAGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCt  >  4:232143/1‑149 (MQ=255)
                                                                                                                                      cctgcgcAGACTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCt  >  3:67454/4‑149 (MQ=255)
                                                                                                                                                |                                                                                                                                          
GCGCCTGCCGCGTTGCGTCAATCCGGACACCGAACGCCTGGCTTTGGGCTTGCTCGAGCGTCAGCTGAAATGGCCGGACACCCTGCGCATCGAACTGCGCGAAGGTAGCCCGAGTGGCCGGTATCTGGCCGGTATCGGCGCAGAGTCTGCGCAGGATGTACGGTGTATCGTGCGCCGCGGCGACGGCTATCGCTACGCCGGTCAAGGTACATCCGGCCCCTACCTGGCGGCACTGTTGGCTGCGCTGGACGAGACGCAGACAGCCGATCTCGGCGATGCCGCT  >  NC_002947/1228935‑1229217

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: ‑