Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,741,748 C→A 12.0% P1376Q (CCA→CAA)  PP_2395 → leucine‑rich repeat‑containing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,741,7480CA12.0% 139.2 / 5.5 51P1376Q (CCA→CAA) PP_2395leucine‑rich repeat‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (19/25);  new base A (2/3);  total (22/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GCTAGACCTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGGCGCATC  >  NC_002947/2741605‑2741894
                                                                                                                                               |                                                                                                                                                  
gCTAGACCTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTg                                                                                                                                                >  5:326962/1‑148 (MQ=255)
 cTAGACCTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGc                                                                                                                                               <  1:391652/148‑1 (MQ=255)
 cTAGACCTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCa                                                                                                                                              <  1:296245/149‑1 (MQ=255)
      ccTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTgg                                                                                                                                         <  2:118870/149‑1 (MQ=255)
      ccTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTg                                                                                                                                          <  4:112956/148‑1 (MQ=255)
       cTGGGCAGGCGTTTATGGCGCCTGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCAATGGCAGGtcga                                                                                                                                        <  1:233938/149‑4 (MQ=255)
       cTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCAATGGCAGGtcga                                                                                                                                        <  2:284332/149‑4 (MQ=255)
         gggCAGGCGTTTATGACACCAGAATACAGTAGACCTGTTCGCTACCCAATGGGCGCTACAGCATAGCAGGGCGCTGAAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCTATTGCAGGTgg                                                                                                                                         >  8:60380/1‑146 (MQ=255)
               gCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAAt                                                                                                                                  >  2:121990/1‑147 (MQ=255)
               gCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAAt                                                                                                                                  >  6:405187/1‑147 (MQ=255)
               gCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAAt                                                                                                                                  >  7:362096/1‑147 (MQ=255)
               gCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGa                                                                                                                                <  2:118275/149‑1 (MQ=255)
                   ttATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCtt                                                                                                                            >  1:266203/1‑149 (MQ=255)
                      tGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTc                                                                                                                          <  6:229990/148‑1 (MQ=255)
                        gcgcCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCtt                                                                                                                        <  3:311602/148‑1 (MQ=255)
                         cgcCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGc                                                                                                                      <  5:405187/149‑1 (MQ=255)
                                    aGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCt                                                                                                                         <  5:109913/135‑1 (MQ=255)
                                    aGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCt                                                                                                                         >  6:109913/1‑135 (MQ=255)
                                     gTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAAt                                                                                                                                  >  4:302097/1‑125 (MQ=255)
                                     gTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAAt                                                                                                                                  <  3:302097/125‑1 (MQ=255)
                                      tAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGtt                                                                                                         <  5:210602/149‑1 (MQ=255)
                                          ccTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTgg                                                                                                     <  8:362096/149‑1 (MQ=255)
                                              ttCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATg                                                                                                  <  6:326962/148‑1 (MQ=255)
                                                 gCTACCCGATGGGCGCTACAGCGTGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGa                                                                                              >  1:361183/1‑149 (MQ=255)
                                                   tACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGAcc                                                                                            >  2:325674/1‑149 (MQ=255)
                                                      ccGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTg                                                                                         <  5:244302/149‑1 (MQ=255)
                                                         aTGGGCGCTACAGCGTGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGcac                                                                                      <  2:361183/149‑1 (MQ=255)
                                                              cgcTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCa                                                                                 <  1:6580/149‑1 (MQ=255)
                                                                cTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCCCAAGCaga                                                                               <  5:375637/149‑1 (MQ=255)
                                                                cTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCaga                                                                               <  7:255967/149‑1 (MQ=255)
                                                                      cATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCAGGATGCGGACCTTGCACAAGCAGAGGCttc                                                                         >  4:301702/1‑147 (MQ=255)
                                                                        tGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCAAAAGAATAGGCtgcgg                                                                       >  5:117939/1‑149 (MQ=255)
                                                                          gCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCtgcggtg                                                                     >  3:273434/1‑149 (MQ=255)
                                                                            aGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCtgcggtgcg                                                                   <  2:377056/149‑1 (MQ=255)
                                                                             gggCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCtgcggtgcgg                                                                  <  4:273434/149‑1 (MQ=255)
                                                                              ggCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCTATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCggg                                                                 <  7:60380/149‑1 (MQ=255)
                                                                                  cTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATg                                                              >  3:54453/1‑148 (MQ=255)
                                                                                           agCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAAcccc                                                    >  6:184753/1‑149 (MQ=255)
                                                                                                       ttGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGc                                        <  4:248519/149‑1 (MQ=255)
                                                                                                       tgggCTTTCAGGAGCGGGCTGAGGTCGTGGCTCGACCTGCAATTGCAGGTGGTATAAATTAGCTTTCTTGCTATCTCAGGCGTCTTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTgt                                        <  1:325674/147‑2 (MQ=255)
                                                                                                            tttCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCt                                   >  5:18293/1‑149 (MQ=255)
                                                                                                                       ggCTGAGGGAGTGTCTCGAGCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGGGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGAc                        <  3:301702/149‑1 (MQ=255)
                                                                                                                            aGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGa                   <  5:184753/149‑1 (MQ=255)
                                                                                                                                      tcGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGc           >  2:104793/1‑147 (MQ=255)
                                                                                                                                      tcGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGc           <  1:104793/147‑1 (MQ=255)
                                                                                                                                       ccaCCTGCAATGGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAgg        >  3:27434/3‑149 (MQ=255)
                                                                                                                                        gACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGgc       >  6:276282/1‑149 (MQ=255)
                                                                                                                                        gACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCCGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGgc       >  5:76239/1‑149 (MQ=255)
                                                                                                                                        caCCTGCAATGGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGgc       >  8:204801/2‑149 (MQ=255)
                                                                                                                                           cTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGGCGCa    <  5:276282/149‑1 (MQ=255)
                                                                                                                                             gCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGGCGCATc  >  5:110594/1‑149 (MQ=255)
                                                                                                                                               |                                                                                                                                                  
GCTAGACCTGGGCAGGCGTTTATGGCGCCAGGATGCAGTAGACCTGTTCGCTACCCGATGGGCGCTACAGCATGGCAGGGCGCTGGAAGGAAGCGAGGTGGGGTTGGCTTTCAGGATCGGGCTGAGGGAGTGTCTCGACCTGCCATTGCAGGTGGGAGAAATGAGCTTTCTTGCGATCTCAGGCGTTCTGGATGCGGACCTTGCACAAGCAGAGGCTGCGGTGCGGGATGCAGAAACCCCGGAAGAGGTTGCCCGCTCCATGGTTGACCGTGAATTCTGGCAGGCGCATC  >  NC_002947/2741605‑2741894

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: ‑