Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 3,220,896 A→T 10.0% L39Q (CTG→CAG)  PP_5539 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029473,220,8960AT10.0% 129.4 / 5.3 50L39Q (CTG→CAG) PP_5539hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (27/17);  new base T (2/3);  total (29/21)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01

GAGGGTGCCCTGCACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTGGGGAAGGTTC  >  NC_002947/3220754‑3221042
                                                                                                                                               |                                                                                                                                                  
gAGGGTGCCCTGCACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAggtgg                                                                                                                                               <  1:273000/148‑1 (MQ=255)
gAGGGTGCCCTGCACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCACCCACCTgggggg                                                                                                                                              >  1:271910/1‑149 (MQ=255)
 aGGGTGCCCTGCACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAggtgggt                                                                                                                                             <  1:13118/149‑1 (MQ=255)
      gCCCTGCACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCACCCACCTGGGGGGCGAgga                                                                                                                                        <  1:321474/149‑2 (MQ=255)
         cTGCACGGGCACCCCCAGCGTGGCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCcgg                                                                                                                                     <  7:351996/149‑1 (MQ=255)
            cACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCACCCACCTGGGGGGCGAggacaaa                                                                                                                                    <  2:271910/147‑6 (MQ=255)
            cACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGGTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCACCCACCTGGGGGGCGAggacaaa                                                                                                                                    <  5:250238/147‑6 (MQ=255)
                       ccAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCg                                                                                                                       >  4:244913/1‑149 (MQ=255)
                       ccAGCGTGTCGATGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCg                                                                                                                       >  2:327443/1‑149 (MQ=255)
                         aGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGtt                                                                                                                     <  2:66293/149‑1 (MQ=255)
                             tgtCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAAt                                                                                                                 <  3:194503/149‑1 (MQ=255)
                             tgtCGATGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAAt                                                                                                                 <  1:327443/149‑1 (MQ=255)
                               tCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAAtt                                                                                                                >  1:300492/1‑148 (MQ=255)
                                     aGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGtc                                                                                                         <  3:134317/149‑1 (MQ=255)
                                       cccATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGtctc                                                                                                       >  6:160260/1‑149 (MQ=255)
                                        ccATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGGGGGTGAGGCCGGCGGTGCCCAAGCCGTTGAATTGATAGTCTcc                                                                                                      >  3:267204/1‑149 (MQ=255)
                                         cATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCCGACGCGTCCGTTGTCTGCCCGCTGATGACGAAACTGCGCCCTTTGTCCTCGACACCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTATAATTGATAGtctc                                                                                                       >  1:265254/1‑148 (MQ=255)
                                         cATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTTATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTccc                                                                                                     <  1:278813/149‑1 (MQ=255)
                                                 aGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAg                                                                                             >  8:314538/1‑149 (MQ=255)
                                                 aGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAg                                                                                             >  1:358469/1‑149 (MQ=255)
                                                   cTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATTCCGAAACTGCGACCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAgg                                                                                            <  2:265254/148‑1 (MQ=255)
                                                   cTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAggg                                                                                           >  1:20641/1‑149 (MQ=255)
                                                           ccAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCt                                                                                   >  2:75460/1‑149 (MQ=255)
                                                            cAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTg                                                                                  <  1:56581/149‑1 (MQ=255)
                                                            cAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTg                                                                                  <  7:124426/149‑1 (MQ=255)
                                                                        cTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGa                                                                      <  1:75460/149‑1 (MQ=255)
                                                                            tCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAg                                                                  >  6:39431/1‑149 (MQ=255)
                                                                             cACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAgg                                                                 >  5:109093/1‑149 (MQ=255)
                                                                             cACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAgg                                                                 >  7:49365/1‑149 (MQ=255)
                                                                                 gcgcC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTg                                                             <  2:300492/149‑1 (MQ=255)
                                                                                 gcgcC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTg                                                             <  2:20641/149‑1 (MQ=255)
                                                                                   gcC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATaa                                                                   <  7:107831/141‑1 (MQ=255)
                                                                                   gcC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATaa                                                                   >  8:107831/1‑141 (MQ=255)
                                                                                          cGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATAcc                                                      >  1:20449/1‑148 (MQ=255)
                                                                                            tCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAg                                                   >  3:368154/1‑149 (MQ=255)
                                                                                             ccGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAGTTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGt                                                  >  4:264044/1‑149 (MQ=255)
                                                                                                  gTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGctc                                              >  4:193848/1‑148 (MQ=255)
                                                                                                      gCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATg                                         >  2:169645/1‑149 (MQ=255)
                                                                                                                 ccGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCt                              >  4:41452/1‑149 (MQ=255)
                                                                                                                   gAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATACGGCCTGCGATACCGAGTGCGCTAATGCATTGCATGcgt                             >  8:155395/1‑146 (MQ=255)
                                                                                                                   gAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCtt                             >  2:91517/1‑148 (MQ=255)
                                                                                                                             ccgccggccTCACCCACCTGGGGGGCGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCtctc                  >  3:49293/8‑149 (MQ=255)
                                                                                                                                   tCCTCGCCCCCCCGGGGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGCCGCGATAAGGCCGGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCgtggt             <  6:20287/148‑1 (MQ=255)
                                                                                                                                     cTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGtggtgg           <  2:358469/148‑1 (MQ=255)
                                                                                                                                      tCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCGTTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTggg          >  3:18253/1‑148 (MQ=255)
                                                                                                                                      tCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTggg          >  5:60259/1‑148 (MQ=255)
                                                                                                                                       cGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTgggg         >  2:73319/1‑148 (MQ=255)
                                                                                                                                         ccccccAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTGGGGAAg      >  8:223654/1‑149 (MQ=255)
                                                                                                                                          cccccAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGCCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTGGGGAAgg     >  4:304919/1‑149 (MQ=255)
                                                                                                                                             ccAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTGGGGAAGGTTc  <  3:244913/149‑1 (MQ=255)
                                                                                                                                               |                                                                                                                                                  
GAGGGTGCCCTGCACGGTCACCCCCAGCGTGTCGGTGAGCCCATATTGGAGCTGGCCACCCAGCCGGGAGAGCTGGTCACCGCGCC‑AGGCGTCCGTTGTCTGCCCGCTGATGCCGAAACTGCGCCCTTTGTCCTCGCCCCCCAGGTGGGTGAGGCCGGCGGTGCCGAAGCCGTTGAATTGATAGTCTCCCTGGTCCAGGGCCATTGCTGGGGTGGTCGCGATAAGGCCTGCGATACCGAGTGCTCTAATGCCTTGCATGCTTCAACTGCTCTCGTGGTGGGGAAGGTTC  >  NC_002947/3220754‑3221042

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: ‑