Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9180AC51.2% 60.5 / 71.6 43intergenic (‑129/+192)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
Reads supporting (aligned to +/- strand):  ref base A (20/1);  new base C (1/21);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 4.61e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.11e-08

AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAG  >  NC_000913/2001783‑2002064
                                                                                                                                        |                                                                                                                                                   
aaTTCACGATAAACAGCCCTGCTTTATATGAGTTATCGGAATGATTATCCGTTTCGGCAGGGTTTTTAATCGG‑ACGATTAGGGGGTGAAATGGGGGGTTATTTGGGGGTTAAAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCg                                                                                                                                       <  2:275457/150‑1 (MQ=255)
 aTTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCggg                                                                                                                                     >  2:422498/1‑151 (MQ=255)
          aaaCAGCCCTGCTTTATATGAGTTATGGGGATGATTATCCGTTTCTGCAGGTTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGTTTTTTTGGGGGTTACAGGTAATTTCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCAca                                                                                                                             <  1:1939647/150‑2 (MQ=255)
             ccgCCCTGCTTTATATGATTTTTCGGAATGATTATCCGTTTCTGCAGGGTTTTTAAGCGG‑ACGATTTGTGGGTGAATGGGGGGTTTATTGGGGGGTTAAAGGTAATTTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTg                                                                                                                          <  1:1187274/148‑1 (MQ=255)
                   tGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACa                                                                                                                    >  2:4043903/1‑150 (MQ=255)
                      gTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                                >  2:4003026/1‑151 (MQ=255)
                       ttATATGAGTTATCGGCATGATTATCCGTTTCTGCGGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAAGGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAAtt                                                                                                                <  2:788146/150‑1 (MQ=255)
                                 tatcgggtggtttttCCGTTTCTGCGGGTTTTTTAAGGGG‑AAGTTAAGGGGGGAAAATGAGGGGTTATTGGGGGGTTACGGGAAAATCCCGGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑g                                                                                                     <  2:3987818/136‑1 (MQ=255)
                                                ccttttCTGCGGGTTTTTTAATGGG‑ACGATTAGGGGGTGAAATGGGGGGTTTTTGGGGGGTTACAGGTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGa                                                                                             <  1:3261619/140‑1 (MQ=255)
                                                 cGTTTCTGCAGGGTTTTTAATAGG‑AAGATTAGGGGGCGAAATGAGGGGTGATTTGGGGGTGACAGGTAAATTGAAGGCTGAAAAAACCGTCGCAGGTGGGGGGGAAGCACGTAGGTGACGAAATGAGCTTAAT‑GTTGACGGAGgcggag                                                                                      >  1:2523658/1‑147 (MQ=255)
                                                   tttCTGCAGGTTTTTTAATCGG‑ACGTTTAGTGGGTAAAATGAGGGTTTATTGGGGGGTTACAGGAAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATgcggc                                                                                       <  2:4030965/146‑1 (MQ=255)
                                                   tttCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTaa                                                                                   >  2:2877933/1‑150 (MQ=255)
                                                   tttCTGCAGGGTTTTAAAGCGG‑AGTATTGGGGGTTAAAATGGGGGGTTTTTGGGGGGTTAAAGGAAAATCCAAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATgcgg                                                                                        <  1:697855/145‑1 (MQ=255)
                                                     tCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACg                                                                                >  2:2545656/1‑151 (MQ=255)
                                                       tGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGcc                                                                              >  1:2693893/1‑151 (MQ=255)
                                                        gCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCt                                                                             >  1:3025212/1‑151 (MQ=255)
                                                        gCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGG‑TACCGGGAAATTCCAAGGAGAAAAAAAACCCCGCGGGGGCGGGGGAAGAAGGTGCTTGCCAATTTCGGTTTATGGTTGCCGGATG‑GGCGGAAACCCCtt                                                                            >  2:1794471/1‑151 (MQ=255)
                                                            ggTTTTTAAACGGAACGATAAGGGGGTAAAAGGGGGGTTTTTTGGGGGGTTACAGAAAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCtt                                                                            <  2:249930/149‑1 (MQ=255)
                                                                tttAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGc                                                                     >  1:601053/1‑151 (MQ=255)
                                                                    aatcgagcgttgagggggTAAAAGGGGGGTTTTTTGGGGGGTTACAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCt                                                                   <  1:4100643/135‑1 (MQ=25)
                                                                       gg‑ACGATTGGTGGGTAAAAGGGGGGTTTTTTTGGGGGTTACAGGTAAATCCCGGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACa                                                                <  1:2377383/149‑1 (MQ=37)
                                                                          aCGATGAGTGGGTGAAATGGGGGTTTATTGGGGGGTTACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa                                                             <  2:1873066/150‑1 (MQ=38)
                                                                              ttAGTGGGTGAAAGGGGGGGTTTTTGGGGGGTTACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAt                                                           <  2:541502/148‑1 (MQ=38)
                                                                                 gggggTGAAAGGAGGGTTTTTTGGGGGGTTAGAGGTAAATTCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCa                                                      <  1:485773/148‑1 (MQ=37)
                                                                                 gTGGGTGAAATGAGGGGTTTTTGGGGGTTTACAGGTAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGc                                                       <  1:2769123/149‑1 (MQ=38)
                                                                                  tGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCaa                                                     >  2:2665615/1‑150 (MQ=255)
                                                                                   gggTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAAt                                                   >  2:403242/1‑151 (MQ=255)
                                                                                     gTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc                                                 >  2:890064/1‑151 (MQ=255)
                                                                                     gTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc                                                 >  1:1271227/1‑151 (MQ=255)
                                                                                         aaTGGGGGTTTATTGGGGGTTTACAGGTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                                             <  2:558509/151‑1 (MQ=37)
                                                                                           tGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATaa                                            >  1:3369050/1‑150 (MQ=255)
                                                                                             aGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAtt                                         >  2:3486797/1‑151 (MQ=255)
                                                                                               ggtttATTTGGGGTTTACAGGAAAATCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGc                                       <  1:1722616/148‑1 (MQ=37)
                                                                                                  ttATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAAt                                    >  2:209656/1‑151 (MQ=255)
                                                                                                             ttaaggtaaaaTTCCGGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTa                          <  1:2498920/142‑1 (MQ=37)
                                                                                                             taaCAGGTAAATCCCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTa                          <  2:773206/148‑1 (MQ=255)
                                                                                                                cAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAACCGCCTTATCCGGCCTACAAAAATGGGCAAATTCAATAAATTGCAATTCAACTTGTAGGcc                      >  1:3107617/1‑151 (MQ=255)
                                                                                                                   gTAAATTCCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGca                      <  1:3062316/148‑2 (MQ=255)
                                                                                                                     aaaTTCCGGGAAAAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTg                    <  1:661490/148‑1 (MQ=255)
                                                                                                                      aaTTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATa                 >  1:3164247/1‑150 (MQ=255)
                                                                                                                           cAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgc            >  1:1929303/1‑150 (MQ=255)
                                                                                                                           cAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgca           <  2:601034/151‑1 (MQ=255)
                                                                                                                            aGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgc            >  2:99186/1‑149 (MQ=255)
                                                                                                                                aaaaaaaacCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgcagcg        <  2:1261776/147‑1 (MQ=255)
                                                                                                                                    aaaacCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAg  <  1:1251775/151‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                                   
AATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAG  >  NC_000913/2001783‑2002064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑