Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 468,056 G→T 17.7% M1M (ATG→ATT) † glnK → nitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP009273468,0560GT17.7% 98.7 / 18.5 51M1M (ATG→ATT) †glnKnitrogen assimilation regulatory protein for GlnL, GlnE, and AmtB
Reads supporting (aligned to +/- strand):  ref base G (14/28);  new base T (4/5);  total (18/33)
Fisher's exact test for biased strand distribution p-value = 7.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.64e-01

TGTGCACTGTCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGG  >  CP009273/467915‑468198
                                                                                                                                             |                                                                                                                                              
tgttcactgtCATACTGCGTGTTCACTTTCAGCCGTCTTAACTCTCTGCGCTCTTTCTCGTGTTTCATGTCTGGCACACCGCTTGCAATACCTTCTCCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTgg                                                                                                                                         <  1:242237/149‑1 (MQ=255)
  tgcactgtCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTg                                                                                                                                       <  1:1300612/149‑1 (MQ=255)
     cctgcCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATGTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCCAATTCTGACCGGAGGGGATCTATGAAGCTg                                                                                                                                          <  2:936031/142‑1 (MQ=255)
       tgtCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGCCCGGAGGGGATCTATGAAGCTGGt                                                                                                                                        >  2:902001/1‑143 (MQ=255)
       tgtCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGt                                                                                                                                        >  2:566054/1‑143 (MQ=255)
         tCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCGTTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGa                                                                                                                                <  1:518276/149‑1 (MQ=255)
                 cGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCaaa                                                                                                                        <  1:861149/149‑1 (MQ=255)
                          tttcaAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAg                                                                                                               <  1:1157011/149‑1 (MQ=255)
                          tttcaAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGGTAATCAAACCATTCAAg                                                                                                               >  1:1063615/1‑149 (MQ=255)
                          tttcaAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAg                                                                                                               <  1:1124255/149‑1 (MQ=255)
                            tcaAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCt                                                                                                             <  1:908392/149‑1 (MQ=255)
                              aaaCTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTgg                                                                                                           <  1:903213/149‑1 (MQ=255)
                               aaCTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCTTTTTTTTTTCACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGGGGGCATCTATGAAACTGGTGCCCGTGCTAATCAAACCATTCaa                                                                                                                >  2:33171/1‑143 (MQ=255)
                                aCTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAg                                                                                                               <  2:328185/143‑1 (MQ=255)
                                  ttcttAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGcc                                                                                                             <  2:811508/143‑2 (MQ=255)
                                   tcttAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTg                                                                                                            <  2:1123516/143‑1 (MQ=255)
                                   tcttAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTg                                                                                                            >  2:1062526/1‑143 (MQ=255)
                                   tcttAACTTCCTGCTCTCTTTCGCGTTGTTCATTGCTGGCACCCCGCTTGCAATACCTTCTGCGGGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCCAGCTGGAAGAc                                                                                                      <  1:118449/149‑1 (MQ=255)
                                    cttAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGATGCTGGTGACCGTGATAATCAAACCATTCAAGCTgg                                                                                                           <  2:702808/143‑1 (MQ=255)
                                      tAACTTCCTGCTCTCTTTCTCGTTTTTCCTTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGaa                                                                                                         <  2:871018/143‑1 (MQ=255)
                                                ctctctTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTg                                                                                               >  2:365658/1‑143 (MQ=255)
                                                 tctctTCTTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGtt                                                                                        <  1:231426/149‑1 (MQ=255)
                                                    ctTTCTCGTTTTTCGTTTCTTTCACGCCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTTGTGACCGTGATAATCAAACCATTCGAGCTGGAAGACGTTCGTGAAGc                                                                                           <  2:1095531/143‑1 (MQ=255)
                                                    ctTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGc                                                                                           <  2:606447/143‑1 (MQ=255)
                                                    ctTGCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGc                                                                                           <  2:606613/143‑1 (MQ=255)
                                                     tttCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACGGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCGTTCAAGCTGGAAGACGTTCGGGAAGCg                                                                                          >  2:325853/1‑143 (MQ=255)
                                                       tctcGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGtt                                                                                        >  2:394020/1‑143 (MQ=255)
                                                           gTTTTTCATTTCTGGCACGCCGCTGGCCATAGCTCCGGCTGTTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCCGGAAGACGTTCGTGAAGCGCTATCt                                                                                    <  2:509497/143‑1 (MQ=255)
                                                            tttttCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTg                                                                             <  1:585559/149‑1 (MQ=255)
                                                              tttCATTTCTGGCACGCCGCTTGCAATACCTTCCTCTCGTAGCAGAACCCTTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGt                                                                           <  1:241297/149‑1 (MQ=255)
                                                                tcatccgtgtcacaCCGCTTGCAATACCTGCGTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTAGGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCAt                                                                               <  2:1004367/133‑1 (MQ=255)
                                                                 cATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGGGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCAtt                                                                              <  2:642562/143‑1 (MQ=255)
                                                                    ttCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAg                                                                     <  1:1064913/149‑1 (MQ=255)
                                                                    ttCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAg                                                                     <  1:1214205/149‑1 (MQ=255)
                                                                    ttCTGGCACACCGCTTGCAATACCTTCTTCGTCCAGCAAAACCAGTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTACGTGAAGCGTTATCTTCCATTGGTATTCAg                                                                     <  1:680259/149‑1 (MQ=255)
                                                                        ggCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTc                                                                       >  2:144354/1‑143 (MQ=255)
                                                                          cacaCCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGTAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAg                                                                     <  2:978003/143‑1 (MQ=255)
                                                                              ccGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCAAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGTTATTCAGGGCCTGACCg                                                           >  1:204665/1‑149 (MQ=255)
                                                                                      aaTACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGaa                                                   <  1:423317/149‑1 (MQ=255)
                                                                                           cttcttCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCCCCGAAGGGaa                                              >  1:483672/1‑149 (MQ=255)
                                                                                            ttcttcGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGaaa                                             <  1:964037/149‑1 (MQ=255)
                                                                                             tcttcGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGAGATCTATGAAGCTGGTGACCGTGATAACCAAACCATTCAAGCTGGAAGCCGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGTAAg                                            >  1:380427/1‑149 (MQ=255)
                                                                                                   tgtAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGGCACCGGAGTGAAAg                                            >  2:592397/1‑143 (MQ=255)
                                                                                                             ccATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGaa                            <  1:403653/149‑1 (MQ=255)
                                                                                                                    ccacgtCTGACCGGGGGGGATCTAGGAAGCGGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGaaa                           <  2:273469/138‑1 (MQ=255)
                                                                                                                       aTTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGcc                  >  1:1047990/1‑149 (MQ=255)
                                                                                                                        ttCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGc                       >  2:193757/1‑143 (MQ=255)
                                                                                                                               cGGAGGGGGTCTATTAAGCTGGTGACCGTGAGGATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGGGAAAGGTTTCGGGCGTCAGAAGGGGCATGCCGa                >  2:632047/1‑143 (MQ=255)
                                                                                                                                      gATCTATTAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCggggg   >  1:379150/1‑149 (MQ=255)
                                                                                                                                       aTCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGCAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCgggggg  >  1:74018/1‑149 (MQ=255)
                                                                                                                                          tATGCAGCTGGTGACCGTGATAATCAACCCATTCAAGCTGTAACACGGGCGTGGAGCGTTATCTTCCATTGTTATTCAGGGCCTGACCGTCCCCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCggg     <  2:321001/143‑1 (MQ=255)
                                                                                                                                             |                                                                                                                                              
TGTGCACTGTCATAGTGCGTTTTCATTTTCAAACTTCTTAACTTCCTGCTCTCTTTCTCGTTTTTCATTTCTGGCACACCGCTTGCAATACCTTCTTCGTGTAGCAGAACCATTACCGAATTCTGACCGGAGGGGATCTATGAAGCTGGTGACCGTGATAATCAAACCATTCAAGCTGGAAGACGTTCGTGAAGCGTTATCTTCCATTGGTATTCAGGGCCTGACCGTCACCGAAGTGAAAGGTTTCGGGCGTCAGAAAGGGCATGCCGAGCTGTACCGGGGGG  >  CP009273/467915‑468198

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑