Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,101,5140GT27.6% 136.2 / 26.6 58intergenic (+84/‑176)sodA/kdgTsuperoxide dismutase (Mn)/2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter
Reads supporting (aligned to +/- strand):  ref base G (7/35);  new base T (16/0);  total (23/35)
Fisher's exact test for biased strand distribution p-value = 3.07e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AACGTGGTGAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATT  >  NC_000913/4101380‑4101642
                                                                                                                                      |                                                                                                                                 
aaCGTGGTGAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATc                                                                                                                              <  1:143375/140‑1 (MQ=255)
  cGTGGTGAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑aa                                                                                                                           >  2:742738/1‑140 (MQ=255)
    tggtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AAtt                                                                                                                         >  2:1039249/1‑140 (MQ=255)
      gtgAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTc                                                                                                                       <  1:1075550/140‑1 (MQ=255)
         aaCTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGACTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCaaa                                                                                                                    <  1:515788/140‑1 (MQ=255)
           cTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAAt                                                                                                                  <  1:16046/140‑1 (MQ=255)
             gggACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATaa                                                                                                                <  2:1165780/140‑1 (MQ=255)
              ggACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATaaa                                                                                                               <  2:227073/140‑1 (MQ=255)
               gACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATC‑AATTTCAAAATaaaa                                                                                                              >  1:1021301/1‑140 (MQ=255)
                 cGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAAc                                                                                                            <  1:433009/140‑1 (MQ=255)
                         cGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGGTC‑AATTTTAAAATAAAAAAAAAGATcc                                                                                                    >  2:238466/1‑140 (MQ=255)
                         cGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCACCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATaa                                                                                                                >  1:244269/1‑128 (MQ=255)
                         cGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCACCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATaa                                                                                                                <  2:244269/128‑1 (MQ=255)
                            cACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGat                                                                                                 <  2:859117/140‑1 (MQ=255)
                            cACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGat                                                                                                 <  1:258796/140‑1 (MQ=255)
                              cGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGGTC‑AATTTTAAAATAAAAAAAAAAAACCGataa                                                                                               >  2:813815/1‑140 (MQ=255)
                              cGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTCAAAATAAAAAAAAAGATCCGataa                                                                                               >  2:1007000/1‑140 (MQ=255)
                                   tGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGataaaaata                                                                                          <  1:37071/140‑1 (MQ=255)
                                         gAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AAATTTAAAATAAAAAAAAAGATCCGataaaaaaaaaaaaa                                                                                    >  2:481506/1‑137 (MQ=255)
                                          aaaaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGc                                                                                   >  1:997364/1‑140 (MQ=255)
                                          aaaaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTTAAAATAAAAAAAAAAATCCGataaaaaaaaaaaaac                                                                                   >  2:568434/1‑136 (MQ=255)
                                           aaaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATC‑AATTTTAAAAAAAAAAAAAAAATCCGataaaaaaaaaaaaacg                                                                                  >  2:280964/1‑135 (MQ=255)
                                            aaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGt                                                                                 <  1:568434/140‑1 (MQ=255)
                                            aaaaTAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGt                                                                                 <  2:177717/140‑1 (MQ=255)
                                                 aatCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCaa                                                                            <  1:1007000/140‑1 (MQ=255)
                                                    cATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTg                                                                         <  2:997364/140‑1 (MQ=255)
                                                       ttGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAtg                                                                      <  1:742738/140‑1 (MQ=255)
                                                        tGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTTAAAAAAAAAAAAATAATCCGATAAAAAAAAAAAAACGGTTTAATTTAtgt                                                                     >  2:247140/1‑140 (MQ=255)
                                                         gccgccTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGGTC‑AATTTTAAAATAAAAACAAAGATCCGATAAAAATAAAACAGCGTTTTAATTGAtgtg                                                                    >  2:492805/1‑140 (MQ=255)
                                                         gccgccTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGAtgtg                                                                    <  1:813815/140‑1 (MQ=255)
                                                            gccTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGtt                                                                 <  2:1021301/140‑1 (MQ=255)
                                                               tgctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTg                                                              <  2:808243/140‑1 (MQ=255)
                                                               tgctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAAAAGCGTTTCAATTGATGTGGgtttt                                                              >  2:708663/1‑139 (MQ=255)
                                                                 ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAAt                                                                           >  1:412802/1‑125 (MQ=255)
                                                                 ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAGATAAAACAGCGTTTCAATTGATGTGGTTTTGAt                                                            <  2:129017/140‑1 (MQ=255)
                                                                 ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAAt                                                                           <  2:412802/125‑1 (MQ=255)
                                                                 ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGAt                                                            <  1:100902/140‑1 (MQ=255)
                                                                 ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGAt                                                            <  1:280964/140‑1 (MQ=255)
                                                                 ctgcAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGAt                                                            <  2:118993/140‑1 (MQ=255)
                                                                         gggCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTa                                                    <  1:636714/139‑1 (MQ=255)
                                                                         aGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTa                                                    <  2:240949/140‑1 (MQ=255)
                                                                           gCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTCAAAATAAAAAAAATGATCCGATAAAAATAAAAAAACGGTTTAATTTATGTGGTTTTTATCACTTTTAtt                                                  >  2:988309/1‑140 (MQ=255)
                                                                                     cGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATT‑AATTTTAAAATAAAAAAAATGATACGATAAAAATAAAACAGCGGTTCAATTTATGTGGTTTTGATCACTTTTATTTATTAaatgc                                        >  2:636714/1‑139 (MQ=255)
                                                                                     cGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTTTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAaatga                                        >  1:1067664/1‑140 (MQ=255)
                                                                                      gCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGAAGGGGGTTTTTTCGTCTCATTTAAAAAAAAAAACAATG‑CCCACGAAAAATAAAAAAAAGTTTTAATTGATGTGGGTTTTATTAAATTTATTGATTTaataaa                                       >  2:549553/1‑140 (MQ=255)
                                                                                       cATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTTAAAATAAAAAAAATGATCCGATAAAAATAAAAAAGCGTTTCAATTTATGTGGGTTTTATCACTTTTATTTATTAaatgaaa                                      >  1:677598/1‑139 (MQ=255)
                                                                                        atatCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAaatgaatg                                     >  1:459268/1‑140 (MQ=255)
                                                                                                agaaaaaaTGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCtt                             <  1:248969/138‑1 (MQ=255)
                                                                                                   aaaaaTGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGt                          >  1:1026300/1‑140 (MQ=255)
                                                                                                    aaaaTGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGtt                         <  2:1007781/140‑1 (MQ=255)
                                                                                                    aaaaTGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGtt                         <  1:988309/140‑1 (MQ=255)
                                                                                                     aaaTGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGttt                        <  1:238466/140‑1 (MQ=255)
                                                                                                         gAACCATCGCCAACGGCGGTGGTTTTTTTTTGATC‑AATTTCAAAATAAAAAAAATGATCCGATAAAAATAAAACAGCGTTTCAATTTATGTGGGTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTTCAt                    >  1:460350/1‑140 (MQ=255)
                                                                                                         gAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCAt                    <  2:459268/140‑1 (MQ=255)
                                                                                                         gAACCATCGCCAACGGCGGTGGGTTTTTTTTGATC‑AATTTTAAAATAAAAAAAAAGATCCGATAAAAAAAAAAAAGCGTTTCAATTTATGTGGTTTTGATCACTTTTTTTTATTAAATGAATGTCTATCTTCGTTTTCAt                    >  2:1109368/1‑140 (MQ=255)
                                                                                                             cATCGCCAACGGCGGTGGTTTTTTTGTGGTC‑AATTTCCAAATAAAAAAAATTAACCGATAAAAATAAAAAAGCGCTTTTATTTATGTGGTTTTTATCACTTTTATTTATTAAATGAATGTCTATTTTTGTTTtcatcact                >  2:248969/1‑138 (MQ=255)
                                                                                                                   cAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGAt          <  2:1026300/140‑1 (MQ=255)
                                                                                                                    aaCGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATg         <  1:5275/140‑1 (MQ=255)
                                                                                                                      cggcggTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCt       <  2:677598/140‑1 (MQ=255)
                                                                                                                       ggcggTTGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTc      <  1:481506/140‑1 (MQ=255)
                                                                                                                           gtggtTTTTTTGTGATC‑AATTTCAAAATAAAAACAAAGATCCGATAAAAATAAAACAGCGTTTCAATTTATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCAtt  >  2:650209/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                 
AACGTGGTGAACTGGGACGAAGCAGCGGCACGTTTTGCGGCGAAAAAATAATCATTTGCCGCCTGCTGCAATGAGGCGTATAGGCCGCATATCAGCTTAAAAAATGAACCATCGCCAACGGCGGTGGTTTTTTTGTGATC‑AATTTCAAAATAAAAACAATGATCCGATAAAAATAAAACAGCGTTTCAATTGATGTGGTTTTGATCACTTTTATTGATTAAATGAATGTCTATCTTCGTTTCCATCAACACTGATGCTCCATT  >  NC_000913/4101380‑4101642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑