Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,423,2900AC42.3% 56.9 / 17.9 54intergenic (+96/+133)yhdZ/rrfFputative amino acid ABC transporter ATPase/5S ribosomal RNA of rrnD operon
Reads supporting (aligned to +/- strand):  ref base A (7/23);  new base C (20/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.08e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTG  >  NC_000913/3423149‑3423429
                                                                                                                                              |                                                                                                                                            
tAAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTGCTGCCCCCCCCCCAccc                                                                                                                                       >  1:867770/1‑148 (MQ=255)
     cAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGGGTCCTTCCCCCCCCCCCCCCGGcc                                                                                                                                   >  1:11761/1‑148 (MQ=255)
     cAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGt                                                                                                                                 <  2:775733/150‑1 (MQ=255)
          cGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTTCCCCCCCCCCCcccgcccggcgttcc                                                                                                                           >  2:161786/1‑144 (MQ=37)
               gAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTCCCCCCCCCCCCCCCGGGCCGTGCTTCGCa                                                                                                                        >  2:951031/1‑149 (MQ=255)
                aGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTGCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACg                                                                                                                    <  1:333847/151‑1 (MQ=255)
                  ggCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCTGCCGCCCCCCTCCGTGGCGGTGTTTCGCCAcagt                                                                                                                   >  2:896252/1‑148 (MQ=25)
                     aTTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGACTCCTGTCCCCCCCCCCCCCCGCCGTTGCtttctacactt                                                                                                                   >  1:432364/1‑139 (MQ=255)
                           aTCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCg                                                                                                          <  2:960092/150‑1 (MQ=255)
                              gCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGGTTCATCCCCCCCCCCCCCCCCGCCGTGTCTTTTCAACGCTCAACTcaccccc                                                                                                      >  1:796416/1‑145 (MQ=255)
                              gCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTcc                                                                                                      <  2:482645/151‑1 (MQ=255)
                                aGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCcg                                                                                                    <  1:440562/151‑1 (MQ=255)
                                    aaTCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGTCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCcggcg                                                                                                 <  1:947978/150‑1 (MQ=255)
                                       ccATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGAt                                                                                              <  1:823727/150‑1 (MQ=255)
                                        cATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCTCCCCCCCCCCCCCCGGCCGGTGCTTCGCAACATTCAAAACCGCTCCccgccggctt                                                                                            >  1:231110/1‑145 (MQ=255)
                                             aTTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCt                                                                                       <  2:360172/151‑1 (MQ=255)
                                             aTTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCt                                                                                       <  2:68758/151‑1 (MQ=255)
                                               tGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTa                                                                                      <  2:401103/150‑1 (MQ=255)
                                                     ttAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCggg                                                                                <  1:4922/150‑1 (MQ=255)
                                                     ttAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCCGCCCCCCCCCCCCCCGGCCGTTTCTTTTCAACGTTCAAATCCGCCCCCCGCGGGTTTGTCCCACTCggg                                                                                >  1:922490/1‑150 (MQ=17)
                                                     ttAGTACGAAAAGCAAAAAGGCCATCCTGTCGGATGGCCTTTCGCTTGATTTGAGGCCTTGCAGTTTATGGCGGTAGCGCTGCCCGCCACCCTCCGGCCCGTTGCGTCGCAACGTTCAAATCCGCGCCCGGCGGATTTGTTCTa                                                                                      <  1:300756/144‑1 (MQ=255)
                                                          tCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTCCCCCCCCCCCCCCCGGCCGTTGCTTCGCAACGCTCAAATCCGCTCCCCGCGGGGTTTTCCtcccccgggggggg                                                                          >  1:964917/1‑138 (MQ=17)
                                                           cGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTCCCCCCCCCCCCCCCGGCCGTTGCTTTGCAAACGTCAAAAACGCCCCCCGCGGGTTTTTTCTACTCcgggggggg                                                                          >  2:653670/1‑144 (MQ=17)
                                                            gAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGtt                                                                        <  2:308054/151‑1 (MQ=255)
                                                                aGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCAcc                                                                    <  1:653603/151‑1 (MQ=255)
                                                                 gCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCg                                                                   <  2:511073/151‑1 (MQ=255)
                                                                   aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTTCTTCCCCCCCCCCCCCCCGCCGCTTCTTCCCCACGCTTCAATCCCCCCCCCGCGGGTTTTTTCCCCTCTGGTGAGTGTTCTccccc                                                                 >  2:123959/1‑148 (MQ=12)
                                                                   aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCg                                                                   <  1:744101/149‑1 (MQ=255)
                                                                   aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCCCCCCCCCCCCCCCCGGGCCGTTGCTTCGCTACGGTCAAATACGCCCCCGGCGGGGTTTTCCCACTCCGGAGAGGGTTCTCCCac                                                                 >  2:843920/1‑151 (MQ=14)
                                                                   aaaaaGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCCTCCCCCCACCCCCCCGGGCGCTGCCTTGCAACGGTTCAATCCCCCCCCCGCCGGGTTGTTCCTCTCGCGagaggggtttccccc                                                                 >  1:741968/1‑140 (MQ=9)
                                                                    aaaaGGCCATCCTTTCGGATGGCCTGTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGaca                                                                <  1:799081/151‑1 (MQ=255)
                                                                     aaaGGCCTGACTCTCGGATTGCCTTACTCTTGTTTTGATGTTTGACTGTTTATGACGGTAGTCTTGTCCGCCGCCCTCCGGGCCGTTGCTTCGCATCGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGac                                                                 <  1:912671/149‑1 (MQ=14)
                                                                          ccttcttttCGTGTGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCAGCCCGCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAaacaac                                                          <  1:162198/145‑1 (MQ=14)
                                                                            aTCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTTCCCGCCCCCCTCCCGGGCGTTGCTTTGCAACGGTTCAAATCGCCCCCCGCGGGTTTGTCCTACCCCGGAGAGGGGTCACCCacaaaaaaaa                                                         >  2:298524/1‑148 (MQ=255)
                                                                               cTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGGCCTTCCCGCCCCCCTCCCGGCCGTTGCTTCTCCACGTTTAAATCCTCTCCCCGCGGGTTTTTCCTACTCCGGGGAGGGTTCCCCCacaaacaa                                                           >  1:21746/1‑145 (MQ=14)
                                                                                tttCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGGGGCCCGCCCGCCCCCCCCCCGGCCGTTGTTTCGCCACGTTCAAAACCGCTCCCGGCGGGGTTGTTCTACTCGCGGGAGGGGTCACCCACAAAACACAGATa                                                     >  1:370560/1‑150 (MQ=255)
                                                                                      aTGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACaaa                                              <  2:361996/151‑1 (MQ=255)
                                                                                      aTGGCCTTCTGCTTAATTTGATGCCTGGCAGTTTATGGCGGGCGTCCTGCCCCCCCCCCCCCCGGCCGGTGGTTTGCAACGATCAAATCCGCCCCCCGCGGGTTTTTTCTTCACCAGCGAGGGTTTACCCACCAACAAAAACTaaaaa                                                 >  1:599427/1‑147 (MQ=0)
                                                                                        ggCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAg                                            <  2:262719/151‑1 (MQ=255)
                                                                                           cTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTTCCCCCCCCCCCCCCGGCCGTTGCTTCGCAACGTTCAAATACCCCCCCCGCGGGTTTTTCCTACTCCGGAGAGTGTTCACCCACAAACAACAGATAAAACAAAAAGcc                                         >  2:841628/1‑151 (MQ=14)
                                                                                               cGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCCCCCACCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGt                                     <  1:356683/151‑1 (MQ=255)
                                                                                                     atttgatGTCTGGCAGTTTATGGCGGGCGTCCTGCCCCCCCCCCCCCGGGGCGGTGCTTCCCAACGTTTAAAACCCCTCCCCGCGGGGTTGTCCCACCCGGGAGAGAGTTTCCCCACAAACCACAGATAAAAAAAAAAGCCCAGTCTTcc                                >  1:81579/1‑150 (MQ=2)
                                                                                                          atGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGa                          <  2:614733/151‑1 (MQ=38)
                                                                                                                ggCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCttt                    <  2:374764/151‑1 (MQ=35)
                                                                                                                   aGTTTATGGCGGGCGTCCTGCCCCCCACCCTCCCGGCCGTTGCTTCGCAACGTTCAAATCCGCCCCCGGCGGGTTTGTCCCACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAAGCCCAGTCTTCCGACTGAGCCTTTTGt                 >  2:80486/1‑151 (MQ=14)
                                                                                                                   aGTTTATGGCGGGCGTCCCTCCCGCCCCCCCCCCGGCCGTTGCTTTGCAACGTTCAAATCCGCTCCCGGCGGGGTTTTCCCACCCGGGAGAGGGGTCACCCACCAAAAAAAGATAAAAAAAAAAACCCAGTCCTCCGGCTGGGCCcttttt                 >  1:333599/1‑149 (MQ=2)
                                                                                                                    gTTTATGTCGGGCGTCCTGCCCGCCCCCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGt                 <  1:747772/150‑1 (MQ=255)
                                                                                                                         tGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGGGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTAtt           >  1:932705/1‑151 (MQ=38)
                                                                                                                         tGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTAtt           >  1:559542/1‑151 (MQ=38)
                                                                                                                          ggcgggcgTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTAttt          <  1:941537/151‑1 (MQ=38)
                                                                                                                             gggcgTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGAt       >  2:549865/1‑151 (MQ=38)
                                                                                                                              ggcgTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATg      <  2:197009/151‑1 (MQ=38)
                                                                                                                              ggcgTCCTGACCGCCACCCTCCGGGCCGTTACTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTCTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGACCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATg      >  1:71242/1‑151 (MQ=255)
                                                                                                                                  tCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTg  >  1:421428/1‑151 (MQ=40)
                                                                                                                                              |                                                                                                                                            
TAAATCAGAGCGTACGAGGGCATTTTTATCGCAGGTAATCCATTAATTGAATGTTAGTTCGAAAAGCAAAAAGGCCATCCTTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTG  >  NC_000913/3423149‑3423429

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: