Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9180AC51.8% 29.6 / 39.7 27intergenic (‑129/+192)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
Reads supporting (aligned to +/- strand):  ref base A (11/2);  new base C (0/14);  total (11/16)
Fisher's exact test for biased strand distribution p-value = 5.98e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-05

GGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGA‑TTATCCGTTTCTGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGG  >  NC_000913/2001772‑2002065
                                                                                                                                                      |                                                                                                                                                   
ggTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGA‑TTATCCGTTTCTGCAGGGGTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAAcccc                                                                                                                                                 >  1:281736/1‑151 (MQ=255)
     agagTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGA‑TTATTCGTTTCTGCAGGGGTTTTAATCGTAAGATT‑AGTGGATGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGCAAAAAACCccgc                                                                                                                                               <  1:102216/148‑1 (MQ=255)
              tCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGA‑TTATCCGTTTCTGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCgggg                                                                                                                                    >  2:333896/1‑150 (MQ=255)
                              tGCGTTATGTGAGTTTCCGGC‑TGATTTTTCCGTTTCCGGAGGTTTTTTAA‑CCGACTCTTAAGTGGGTAAATTGAGGGTTTATTTGGGGGTTA‑AAGGTAATTG‑CGAGCCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTg                                                                                                                          <  1:169262/144‑1 (MQ=255)
                               gtgTTAGATGGGTTATGGGGATGA‑TGATCGTTTTCTACGGGGTTTTTAAGCGGCGGTTT‑GGTGGGTAAATGGGGGGGTTTTTTGGGGGGTA‑CAGTTAATTT‑CCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaaa                                                                                                                  <  1:222434/149‑1 (MQ=255)
                               gCGTTATATGAGTTATCGGCATGA‑TTATCCGTTTCTGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACaa                                                                                                                   >  2:120681/1‑150 (MQ=255)
                                        gAGTTATCGGCATTA‑TTATCCGTTTCTGCAGGGTTTTTAATAGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGCAAAAAACCCCGCCGGTGGCGGGGAAGAACGTTGCTGATCAATCGCGCttt                                                                                                         >  1:246867/1‑151 (MQ=255)
                                                ggCATGA‑TTATCCGTTTCTGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGcc                                                                                                 >  2:371019/1‑151 (MQ=255)
                                                   aTGA‑TTATCCGTTTCTGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCgg                                                                                               >  1:260054/1‑150 (MQ=255)
                                                               tttCTGAGGGTTTTTTAATCGGACGATT‑AGGGGGAAAAATGGGGGGTTTTTTGGGGGTTA‑AAGGAAAATT‑CCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGt                                                                                      <  1:370879/148‑1 (MQ=255)
                                                                   tGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGcc                                                                               >  2:217844/1‑151 (MQ=255)
                                                                    gCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCt                                                                              >  2:152076/1‑151 (MQ=255)
                                                                      aGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCtt                                                                             >  2:37910/1‑150 (MQ=255)
                                                                       gggTTTTTAATCGGACGATG‑AGTGGGTGAAAGGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTa                                                                            <  1:180317/150‑1 (MQ=255)
                                                                        ggTTTTTAATCGGACGATT‑AGTGGGTAAAATGGGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATc                                                                          <  1:177354/151‑1 (MQ=255)
                                                                                   ggACGATT‑AGTGGGTAAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATC‑CCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACa                                                                 <  2:14288/149‑1 (MQ=255)
                                                                                    ggccgataggTGGGTGAAAGGA‑GGGTTTTTTGGGGGTTA‑ACGGGAAATTCCCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACa                                                                 <  2:64357/140‑1 (MQ=25)
                                                                                     aCGATT‑TGTGGGGAAAATGGGGGTTTTTGTGGGGGTTA‑CAGAAAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa                                                              <  2:141155/150‑1 (MQ=37)
                                                                                         tt‑AGTGGGTAAAATGAGGGTTTATTGGGGGTTTA‑CAGGAAAATT‑CCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAAt                                                            <  2:306661/148‑1 (MQ=37)
                                                                                                  tGAAATGGGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc                                                  <  1:45100/150‑1 (MQ=255)
                                                                                                     aaTGAGGGTTTTTTTGGGGTTTA‑CAGATAAATC‑CCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                                              <  1:363067/151‑1 (MQ=37)
                                                                                                        gAGGGTTTATTTGGGGGTTA‑CAGGAAAATC‑CCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATaa                                             <  2:146754/149‑1 (MQ=37)
                                                                                                         aGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAAt                                           >  1:11829/1‑150 (MQ=255)
                                                                                                              ttATTTCGGGGTAA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGAGGGGAAGAACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTACATAAAtt                                          >  1:383217/1‑146 (MQ=37)
                                                                                                                tagtGGGGGTTACCAGAAAACTT‑CCCGTAACAACAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTCTATGTTGCCAGATGCGGCGTAAACGCCTTAGCCGGCCTACAAAAATGTCCAAATTCAATAAATAGCa                                       <  1:84421/145‑1 (MQ=21)
                                                                                                                    gggtgTTA‑AAGTAAAATC‑CCAGGCAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGTCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAAcg                               <  1:391563/151‑2 (MQ=25)
                                                                                                                    gggggTTA‑AAGTTAAATC‑CCAGGAAAAAAAAACCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACt                               <  1:209523/151‑1 (MQ=37)
                                                                                                                                    aattcaggaaaaaaaaaaaCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATaa                 <  1:121666/139‑1 (MQ=255)
                                                                                                                                                    aaaCCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAgg  >  1:137845/1‑150 (MQ=255)
                                                                                                                                                      |                                                                                                                                                   
GGTATAGAGTGAATTCACGATAAACAGCCCTGCGTTATATGAGTTATCGGCATGA‑TTATCCGTTTCTGCAGGGTTTTTAATCGGACGATT‑AGTGGGTGAAATGAGGGGTTATTTGGGGGTTA‑CAGGTAAATT‑CCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGG  >  NC_000913/2001772‑2002065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑