Predicted mutation
evidence seq id position mutation annotation gene description
RA CP009273 4,390,235 T→A I44N (ATC→AAC)  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
*CP0092734,390,2350TA98.0% 149.9 / NA 51I44N (ATC→AAC) hfqglobal sRNA chaperone; HF‑I, host factor for RNA phage Q beta replication
Reads supporting (aligned to +/- strand):  ref base T (0/1);  major base A (30/19);  minor base C (1/0);  total (31/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

ATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATA  >  CP009273/4390089‑4390378
                                                                                                                                                   |                                                                                                                                               
ataAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAAcc                                                                                                                                               <  1:112874/149‑1 (MQ=255)
     gAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATAGAGTCTTTTGATCAGTTCGTGAACCTGTTg                                                                                                                                          >  1:636239/1‑149 (MQ=255)
          gagagaATGGCTAAGGGGCAATCTTTACAAGGTCCGTTACTGAACGCACTGCGTCGGGA‑AGGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAGGCTGCAAGGGCACATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGaaaac                                                                                                                                     >  1:392690/1‑148 (MQ=255)
                aTGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTAACACTGTTGCAAAACACGGt                                                                                                                               >  1:28078/1‑149 (MQ=255)
                  ggCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCa                                                                                                                             <  2:386215/149‑1 (MQ=255)
                     tAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGcc                                                                                                                          >  2:774326/1‑149 (MQ=255)
                       aGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCGGCTAg                                                                                                                        >  1:448606/1‑149 (MQ=255)
                            cAATCTTTACAAGATCCGTTCCTGCCAGACGTGCGCCAGAA‑ACGTGCTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAACTCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGCCAGCCAGATGGt                                                                                                                   >  1:746993/1‑149 (MQ=255)
                                 tttACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACa                                                                                                              >  2:323519/1‑149 (MQ=255)
                                       aGATCCGTTCCTGAACGCACTGCGTCGGGACAGCTGTTGTTG‑GTCGATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCAcg                                                                                                        >  2:766835/1‑149 (MQ=255)
                                                ccTGACCGCACTTCGTCGGGA‑ACGGGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCTGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTa                                                                                               <  1:267577/149‑1 (MQ=255)
                                                  tGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACt                                                                                             <  1:738589/149‑1 (MQ=255)
                                                  tGAACGCACTGCGTAAGGA‑ACGTGTTCCTGTTTCTATTTATTTGGTGATTGGTATTAAGTTGCAAGGGCAAATCGTGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACt                                                                                             <  2:630730/149‑1 (MQ=255)
                                                   gAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACtg                                                                                            >  2:406317/1‑149 (MQ=255)
                                                          cTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGCGCACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTccc                                                                                     <  1:88136/149‑1 (MQ=255)
                                                            gCGTCGGGA‑AAATGTAACATTTTCTATTTATTTGGTGAAGGGTATTACGCTGCAAGGGCAAATCGAGTCTTTTAGTCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGt                                                                                   >  1:92499/1‑149 (MQ=255)
                                                               tCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTACGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGtctc                                                                                <  2:586688/149‑1 (MQ=255)
                                                                cGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGAGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCg                                                                               >  1:453385/1‑149 (MQ=255)
                                                                          gtTCCAGTTTCTATTTATTTGGTGAATGGTATTAATCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAGCACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTtc                                                                      <  2:380528/149‑1 (MQ=255)
                                                                             ccAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACACGCACGCGATTTCTACTGTTGTCCCGTCTCGTCCGGCTtctcg                                                                   >  1:771919/1‑148 (MQ=255)
                                                                             ccAGTTTCTATTTACTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCtca                                                                   <  1:690390/149‑1 (MQ=255)
                                                                              cAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCtcat                                                                  >  2:627540/1‑149 (MQ=255)
                                                                                    cTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGt                                                            <  1:406317/149‑1 (MQ=255)
                                                                                    cTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGt                                                            >  1:225730/1‑149 (MQ=255)
                                                                                     tatttattTGGTGAATGGTATTAAGCTGCAAGGGCAAGTCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGTCAGACGACAATCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTa                                                           >  2:563960/1‑149 (MQ=255)
                                                                                      atttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACCGTaa                                                          >  1:564583/1‑149 (MQ=255)
                                                                                       tttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCACACGGTTTCTAATCCAAGTaac                                                         >  2:358800/1‑149 (MQ=255)
                                                                                       tttatttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCGCGCCCGGTTTCTCATCACAGTaac                                                         <  2:577205/149‑1 (MQ=255)
                                                                                          atttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTaacaac                                                      <  1:374205/149‑1 (MQ=255)
                                                                                          atttGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACAAGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTTATCACAGTaccaac                                                      >  2:101131/1‑149 (MQ=255)
                                                                                               gTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATGACAGTAACAACGCCgg                                                 >  1:214428/1‑149 (MQ=255)
                                                                                               gTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTATTTTGGTCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGCTGGTTTACAAGCACGCGATTTCTAATGTTATCCCATCTCGCCCGGTTTCTACTCACAGTAACAACGCCgg                                                 >  2:377116/1‑149 (MQ=255)
                                                                                                  aaTGGTATTAAGCTGCAAGGGCAAATCGATTCCTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGAGGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTgg                                              <  2:2548/149‑1 (MQ=255)
                                                                                                  aaTGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACTGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTgg                                              >  2:8623/1‑149 (MQ=255)
                                                                                                        aTTAAGTAGCAAGGGCAAATCCATGCTTTTGATCAGTTCCTGAACCTGGTGACAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTATTTTTCTCCCGTCTCGCCCGGTTTCGCATCACAGTAACAACGCCGGTGGCGGTAc                                        <  1:418435/149‑1 (MQ=255)
                                                                                                           aaGCTGCAAGGGCAAATCGAGTCTTTTTATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACcag                                     <  1:721349/149‑1 (MQ=255)
                                                                                                                 cAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTaa                               >  2:393133/1‑149 (MQ=255)
                                                                                                                     ggCAAATCGAGCCTCTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTAc                           <  2:61981/149‑1 (MQ=255)
                                                                                                                        aaaTCGAGTCTTTTGATCAGTTCGTGTATCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcat                        <  2:277575/149‑1 (MQ=255)
                                                                                                                          aTCGAGGCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACcaaca                      >  1:187002/1‑149 (MQ=255)
                                                                                                                              aGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGt                  <  1:366408/149‑1 (MQ=255)
                                                                                                                              aGTCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGt                  >  2:588940/1‑149 (MQ=255)
                                                                                                                                tCTTTTGATCAGTTCGTGAACCTGTTGAAAAACAGGGTCAGCCAGATGGTTTACAAGCAAGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGGAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGCag                >  1:545590/1‑149 (MQ=255)
                                                                                                                                tCTTTTGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGCGGCGGAACCAGCAGAAACTACCATCAAGGTag                >  2:270503/1‑149 (MQ=255)
                                                                                                                                  ttttGATCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTagca              >  2:393904/1‑149 (MQ=255)
                                                                                                                                       aTCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAgcgcg         >  2:535346/1‑149 (MQ=255)
                                                                                                                                        tCAGTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTACCTACCATCATGGTAGCCgagcgc        >  1:549148/1‑149 (MQ=255)
                                                                                                                                         acgTTCGTGAACAGGTTGAAAAACTCGTTCAGCCAGATGGTTTACAAGCATGCGATTTCTACTGCTGTCCCGTCTCGCCCGGGTCCTCATCACAGTAACCACGCCGGTGGCGGTACCAGCAGTAACTACCATCATTGTAGCAGCGCGCa       <  1:220420/147‑1 (MQ=255)
                                                                                                                                           gTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGa     >  1:636498/1‑149 (MQ=255)
                                                                                                                                           gTTCGTGAACCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGa     >  1:143664/1‑149 (MQ=255)
                                                                                                                                              cGTGATCCTGTTGGAGATCACGGTCTGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCACGTCTCGCCCGGTTTCTCATCACAGTAGCAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATa  <  2:149096/149‑1 (MQ=255)
                                                                                                                                                   |                                                                                                                                               
ATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCGGGA‑ACGTGTTCCAGTTTCTATTTATTTGGTGAATGGTATTAAGCTGCAAGGGCAAATCGAGTCTTTTGATCAGTTCGTGATCCTGTTGAAAAACACGGTCAGCCAGATGGTTTACAAGCACGCGATTTCTACTGTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATA  >  CP009273/4390089‑4390378

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑