Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9110GA42.2% 46.4 / 19.6 45intergenic (‑122/+199)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
Reads supporting (aligned to +/- strand):  ref base G (22/4);  new base A (0/19);  total (22/23)
Fisher's exact test for biased strand distribution p-value = 4.26e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCA  >  NC_000913/2001762‑2002055
                                                                                                                                                      |                                                                                                                                                 
cacCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAg                                                                                                                                                   <  1:1484374/150‑1 (MQ=255)
 acCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGaa                                                                                                                                                 <  1:2182465/151‑1 (MQ=255)
 acCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGa                                                                                                                                                  >  1:2689713/1‑150 (MQ=255)
                     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)
                                                                                                                                                      |                                                                                                                                                 
CACCTTCAGCGGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGATTATCCGTTTCTGCAGGGTTTTTAATCGG‑ACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTAT‑GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCA  >  NC_000913/2001762‑2002055

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: ‑