Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 2,139,637 C→A 9.8% Q162H (CAG→CAT)  PP_5481 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029472,139,6370CA 9.8% 154.6 / 6.5 51Q162H (CAG→CAT) PP_5481hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (20/26);  new base A (3/2);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 6.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01

CTAGGGGTGTCGGATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGAAGGTCAGCTCGTC  >  NC_002947/2139490‑2139783
                                                                                                                                                    |                                                                                                                                                  
cTAGGGGTGTCGGATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCAc                                                                                                                                                    <  5:139877/148‑1 (MQ=255)
        gtCGGATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGcc                                                                                                                                            >  6:299677/1‑148 (MQ=255)
         tCGGATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCCGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCAGTGGCGTCGTCGCCAATGCCg                                                                                                                                               <  6:33485/144‑1 (MQ=255)
         tCGGATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCCGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCAGTGGCGTCGTCGCCAATGCCg                                                                                                                                               >  5:33485/1‑144 (MQ=255)
           ggATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGcccacc                                                                                                                                        <  3:272543/149‑1 (MQ=255)
            gATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGcccaccc                                                                                                                                       <  8:279845/149‑1 (MQ=255)
                         gctcGGCGATCACCTTGATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGTCACTGCCGGCCCACCCACCAGCGCCAGTa                                                                                                                          <  4:257920/146‑1 (MQ=255)
                               cGATCACCTTCATGCTGGTGGCCACTGTGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAt                                                                                                                    <  1:76328/149‑1 (MQ=255)
                                    aCCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCGTGCGGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCGTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAtggtg                                                                                                                <  8:167669/148‑1 (MQ=255)
                                      cTTCATGCTGGTGGCTACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAtggtg                                                                                                                >  6:10182/1‑146 (MQ=255)
                                         cATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGaa                                                                                                           <  2:310751/148‑1 (MQ=255)
                                          aTGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGaa                                                                                                                       <  2:124248/135‑1 (MQ=255)
                                          aTGCTGGTGGCCACTGCGGTGCGCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGCCGCCACTGCCGGCCCACCCCCCAGCGCCAGTAGAACATGGTGGAGAAg                                                                                                          >  3:171396/1‑148 (MQ=255)
                                             cTGGTGGCTACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAg                                                                                                       <  5:10182/148‑1 (MQ=255)
                                                    ccACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGAt                                                                                               >  6:126247/1‑149 (MQ=255)
                                                            gTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGca                                                                                       <  6:8391/149‑1 (MQ=255)
                                                               ctctACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGcacca                                                                                    <  6:350814/149‑1 (MQ=255)
                                                                tctACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGcaccac                                                                                   >  7:153242/1‑149 (MQ=255)
                                                                 ctACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGcacc                                                                                     >  3:132860/1‑146 (MQ=255)
                                                                 ctACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGcacc                                                                                     <  4:132860/146‑1 (MQ=255)
                                                                    cGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCAcgccg                                                                               >  1:311569/1‑149 (MQ=255)
                                                                    cGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCAcgccg                                                                               >  1:19728/1‑149 (MQ=255)
                                                                         tttGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCacac                                                                          <  1:163251/149‑1 (MQ=255)
                                                                            gCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCAcaccac                                                                       >  2:236939/1‑149 (MQ=255)
                                                                            gCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCAcaccac                                                                       >  1:177881/1‑149 (MQ=255)
                                                                               ttCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAtggtg                                                                                                                >  5:135580/1‑105 (MQ=255)
                                                                               ttCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAtggtg                                                                                                                <  6:135580/105‑1 (MQ=255)
                                                                                 cGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCAccgag                                                                   <  2:19728/148‑1 (MQ=255)
                                                                                   cTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCAccgagcc                                                                 >  3:83378/1‑148 (MQ=255)
                                                                                        tGGTCAGCGGCCGCGGCATGCGGGCCTTGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCAccgagccgag                                                              >  1:198362/1‑147 (MQ=255)
                                                                                          gTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTTGCTACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCa                                                            <  5:299677/146‑1 (MQ=255)
                                                                                                  ccGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGc                                                 <  4:83378/149‑1 (MQ=255)
                                                                                                  ccGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGc                                                 >  4:193292/1‑149 (MQ=255)
                                                                                                    gcgGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAt                                                                                                                    >  3:121020/1‑80 (MQ=255)
                                                                                                    gcgGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACAt                                                                                                                    <  4:121020/80‑1 (MQ=255)
                                                                                                    gcgGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACGGCCGGCCCACCCACCCGCGCCAGTAGCCGATGGTGGAGAAGTAGCCAAGGCAGCCCCCCCCCCCGCCTCACACCACCCCGCCGAGAAGGAAGGGTTGcaa                                               >  8:190348/1‑147 (MQ=255)
                                                                                                             gggCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGa                                      <  1:236939/149‑1 (MQ=255)
                                                                                                                cc‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAg                                   <  5:126247/149‑1 (MQ=255)
                                                                                                                         cTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGc                                                 <  6:244439/127‑1 (MQ=255)
                                                                                                                         cTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGc                                                 >  5:244439/1‑127 (MQ=255)
                                                                                                                           tGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAg                                                                                                       >  6:270052/1‑71 (MQ=255)
                                                                                                                           tGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAg                                                                                                       <  5:270052/71‑1 (MQ=255)
                                                                                                                                cGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCATCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCa                    >  6:168687/1‑149 (MQ=255)
                                                                                                                                  gCAGTGGCGTCGTCGCCAATGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACt                  >  8:124679/1‑149 (MQ=255)
                                                                                                                                       ggCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGaa              <  3:193292/148‑1 (MQ=255)
                                                                                                                                       ggCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGaa              <  8:153242/148‑1 (MQ=255)
                                                                                                                                          gtcgtcgCCAATGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCgg                           >  6:26669/6‑132 (MQ=255)
                                                                                                                                          gtcgtcgCCAATGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCgg                           <  5:26669/127‑1 (MQ=255)
                                                                                                                                                 ccACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGAAGGTCAGCtcgt   <  2:198362/149‑1 (MQ=255)
                                                                                                                                                  taCTGCCGGCTCACTCAGCATCGCTAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGAAGGTCAGCtcgtc  <  6:253497/148‑1 (MQ=255)
                                                                                                                                                  cACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGAAGGTCAGc       <  7:232486/144‑1 (MQ=255)
                                                                                                                                                  cACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGAAGGTCAGc       >  8:232486/1‑144 (MQ=255)
                                                                                                                                                    cTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATGCACTGGAAGGTCAGCtcgtc  >  5:253497/1‑147 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
CTAGGGGTGTCGGATATCAGCATTGGCACGGCGATCACCTTCATGCTGGTGGCCACTGCGGTGCTCTACGTTGTTTGCGTTCGCTTGCTGGTCAGCGGCCGCGGCATGCGGGCC‑TGAAGCCTTGCACCGGCATTGGCGACGACGCCACTGCCGGCCCACCCACCAGCGCCAGTAGAACATGGTGGAGAAGTAGGCAAGGATGCCCAGCACCACGCCGCACACCACCGAGCCGAGCAGGAAGGGTTGCCACAGCGTCGACAGCTGGTCGGTGATCCACTGGAAGGTCAGCTCGTC  >  NC_002947/2139490‑2139783

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: ‑