Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_pgi 4,399,663 T→G F39C (TTT→TGT)  hfq → global sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_pgi4,399,6630TG98.1% 175.6 / NA 53F39C (TTT→TGT) hfqglobal sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base G (26/26);  minor base C (1/0);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAG  >  NC_000913_3_pae_pgi/4399518‑4399807
                                                                                                                                                 |                                                                                                                                                
ggaCAAATAAGCATAAAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTTGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGa                                                                                                                                               <  2:961846/147‑1 (MQ=255)
 tACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGAt                                                                                                                                              <  1:1050922/149‑1 (MQ=255)
    aaaTAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAg                                                                                                                                           >  1:644089/1‑149 (MQ=255)
    aaaTAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGGTCCTGAAAGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAACTCGAGTCTTGTGTTCAg                                                                                                                                           >  2:46815/1‑149 (MQ=255)
         aggatatAAGGAAAAGAGAGATGGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGt                                                                                                                                      <  2:318320/146‑1 (MQ=255)
             tataAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATc                                                                                                                                  <  1:521119/149‑1 (MQ=255)
              ataAGGGAAAGAGAGAATGGCGAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTAGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATcc                                                                                                                                 >  2:366435/1‑149 (MQ=255)
                         agagaATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGa                                                                                                                           <  1:336564/144‑1 (MQ=255)
                         agagaATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGa                                                                                                                           >  2:336564/1‑144 (MQ=255)
                                 gCTAAGGGGCAATCTTTACAAGAGCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAg                                                                                                              <  2:374100/149‑1 (MQ=255)
                                                 tACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAg                                                                                              >  2:713003/1‑149 (MQ=255)
                                                  aCAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGc                                                                                             >  2:957783/1‑149 (MQ=255)
                                                       aTCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCAcgcg                                                                                        >  1:10761/1‑149 (MQ=255)
                                                           gTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATGTATTTGGGGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGGTCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACACGAAcgcaaact                                                                                    >  2:136682/1‑144 (MQ=255)
                                                                tGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACt                                                                               <  1:593418/149‑1 (MQ=255)
                                                                     gCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTCTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGATTTACAAGCTCGCGACTTCTACtttcgt                                                                          >  2:52417/1‑144 (MQ=255)
                                                                         tGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCg                                                                      >  1:11733/1‑149 (MQ=255)
                                                                           cGTCGGTAGCGTGTTCAATGTTCTATTTATTTGGTGAAGGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAATCACGGTAAGCCAGATGGTTTACAAGCACTCGATTTCTACTGTTGTCCCGtc                                                                    <  1:479982/149‑1 (MQ=255)
                                                                                    cGTGCTCCAGTTGCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGt                                                           <  1:403203/149‑1 (MQ=255)
                                                                                     gtgtTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGtt                                                          >  2:998459/1‑149 (MQ=255)
                                                                                         tCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTtctc                                                      <  1:713003/149‑1 (MQ=255)
                                                                                         tCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTtctc                                                      <  1:787667/149‑1 (MQ=255)
                                                                                             gTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCtcatca                                                  <  2:480972/149‑1 (MQ=255)
                                                                                             gTTTCTATTTAATTGGAGAATGGTATTAAGCTGCAAGCGCACCTCGATTCTTGAGAAAAGATCGTAAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCtcatca                                                  >  2:1011093/1‑149 (MQ=255)
                                                                                              tttCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCtcatca                                                  >  1:703290/1‑148 (MQ=255)
                                                                                              tttCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCtcatca                                                  <  2:703290/148‑1 (MQ=255)
                                                                                               ttCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATcaca                                                <  1:84912/149‑1 (MQ=255)
                                                                                               ttCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAAGCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATcaca                                                <  2:644089/149‑1 (MQ=255)
                                                                                                tCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAg                                               <  2:283982/149‑1 (MQ=255)
                                                                                                 cTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGTTCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCGGGTTTCtcttcttagt                                              >  2:255402/1‑144 (MQ=255)
                                                                                                 cTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATc                                                                                                                                  >  1:758154/1‑65 (MQ=255)
                                                                                                 cTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATc                                                                                                                                  <  2:758154/65‑1 (MQ=255)
                                                                                                   atttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTaa                                            <  1:998459/149‑1 (MQ=255)
                                                                                                   atttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGAGCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTaa                                            >  1:36373/1‑149 (MQ=255)
                                                                                                            gTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCgg                                   >  1:408419/1‑149 (MQ=255)
                                                                                                             tGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACCACGCCGGt                                  >  2:640096/1‑149 (MQ=255)
                                                                                                                aTGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCCTCCCAGTACCAACGCCGGTGGc                               >  2:31164/1‑149 (MQ=255)
                                                                                                                 tGGTATTAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTGATCACCTTAACAACGCCGGTGGCg                              >  2:818524/1‑149 (MQ=255)
                                                                                                                     agtAAGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTAc                          <  2:782710/147‑1 (MQ=255)
                                                                                                                        aaGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcag                       <  2:11733/149‑1 (MQ=255)
                                                                                                                         aGCTGCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcagc                      >  1:676538/1‑149 (MQ=255)
                                                                                                                          ggtGCAAGGGCAAATCGAGTTTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCGGGTAGCGCATCACAGTAACAACGCCGGTGGCGGTACcagca                     <  1:255402/147‑1 (MQ=255)
                                                                                                                             gCAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTa                  >  2:866300/1‑149 (MQ=255)
                                                                                                                              cAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTaa                 <  1:401426/149‑1 (MQ=255)
                                                                                                                              cAAGGGCAAATCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTAAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAGCGCCGGTGGCGGTACCAGCAGTaa                 >  1:696180/1‑149 (MQ=255)
                                                                                                                               aaGTGCAAACTGAGTCTGGTGATGCGTTCGCTGTCCTGTTTAAGAGCACGGTCAGCCAGATGGTTTACAAGCACGCGATGTCTACTGTTGTCCCGGCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAAc                <  1:136682/149‑1 (MQ=255)
                                                                                                                                     aaaTCGAGTCTTGTGATTAGTTCGTGATCCTGATGAAACGCGGGGATGCTCAAATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcat          <  1:511234/149‑1 (MQ=255)
                                                                                                                                     aaaTCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcat          >  1:990074/1‑149 (MQ=255)
                                                                                                                                     aaaTCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAAAACGGTAAGCCAGATGGTTTACAAGTATGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTAccct          >  1:420130/1‑147 (MQ=255)
                                                                                                                                        tCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTACCAACGCCGGTGGCGGTACCAGCAGTAACTACcatcat       >  1:195298/1‑149 (MQ=255)
                                                                                                                                        tCGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcatcat       >  1:178966/1‑149 (MQ=255)
                                                                                                                                         cGAGTCTTGTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATg      <  2:178966/149‑1 (MQ=255)
                                                                                                                                             tCTTGTGATTAGTTCGTGATCCTGCTGAAGAACACGTTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTag  <  1:46815/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                                
GTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGAACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAG  >  NC_000913_3_pae_pgi/4399518‑4399807

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑