Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,001,983 A→T 11.1% intergenic (‑194/+127) fliA ← / ← fliC RNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,001,9830AT11.1% 110.0 / 4.6 36intergenic (‑194/+127)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein (flagellin)
Reads supporting (aligned to +/- strand):  ref base A (17/15);  new base T (2/2);  total (19/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGAC  >  NC_000913/2001838‑2002128
                                                                                                                                                 |                                                                                                                                                 
tGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACg                                                                                                                                                >  3:328389/1‑149 (MQ=255)
               cGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCt                                                                                                                                   >  3:1147116/1‑147 (MQ=255)
               cGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCt                                                                                                                                   <  4:1147116/147‑1 (MQ=255)
                  aCGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGcc                                                                                                                                              >  3:1110514/1‑133 (MQ=255)
                  aCGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGcc                                                                                                                                              <  4:1110514/133‑1 (MQ=255)
                         gTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                                                                                                   <  1:589514/121‑1 (MQ=255)
                         gTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTaa                                                                                                                                                   >  2:589514/1‑121 (MQ=255)
                                   tGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATa                                                                                                             >  2:1399256/1‑149 (MQ=255)
                                               tGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCa                                                                                                 <  1:1399256/149‑1 (MQ=255)
                                                                ttCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc                                                                                                                 <  3:1258835/116‑1 (MQ=255)
                                                                ttCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTACCCGGCCTACAAAAATGTGCAAATTc                                                                                                                 >  4:1258835/1‑116 (MQ=255)
                                                                         gAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc                                                                                                                 <  4:1312315/107‑1 (MQ=255)
                                                                         gAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTc                                                                                                                 >  3:1312315/1‑107 (MQ=255)
                                                                               ttccccGCCACCGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCaa                                                                                                               <  2:489099/101‑1 (MQ=25)
                                                                               ttccccGCCACCGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCaa                                                                                                               >  1:489099/3‑103 (MQ=21)
                                                                                  cccGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGa                                                                                   >  1:768472/1‑128 (MQ=255)
                                                                                  cccGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGa                                                                                   <  2:768472/128‑1 (MQ=255)
                                                                                   ccgccgGTGGCGGGGAAGCACGTTGCTGCCAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaca                                                                                                                             >  1:762138/1‑83 (MQ=255)
                                                                                   ccgccgGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACaaaa                                                                                                                             <  2:762138/85‑1 (MQ=255)
                                                                                   ccgccgGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAAt                                                             <  4:328389/149‑1 (MQ=255)
                                                                                     gccaccggCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAAttt                                                           >  4:844665/7‑149 (MQ=255)
                                                                                              ggggAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATc                                                                    >  4:1147107/1‑131 (MQ=255)
                                                                                              ggggAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATc                                                                    <  3:1147107/131‑1 (MQ=255)
                                                                                                             tGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGcc                                                                                      <  4:1017775/98‑1 (MQ=255)
                                                                                                             tGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAAGTCAATAAATTGCAATTCAACTTGTAGGcc                                                                                      >  3:1017775/1‑98 (MQ=255)
                                                                                                                  aaTTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAgg                              <  3:844665/149‑1 (MQ=255)
                                                                                                                        gcTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACaa                        >  3:91257/1‑149 (MQ=255)
                                                                                                                                  gCCGGATAAGGCGTTTACGCCGCATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgcagc                                                                         <  1:1237252/90‑1 (MQ=18)
                                                                                                                                  gCCGGATAAGGCGTTTACGCCGCATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAagcgcagc                                                                         >  2:1237252/1‑90 (MQ=18)
                                                                                                                                      gataaggcgTTTACGCCGCATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgca          >  3:868466/6‑149 (MQ=37)
                                                                                                                                       ataaggcgTTTACGCCGCATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGtc                                           <  4:1288710/111‑1 (MQ=25)
                                                                                                                                         gcggcgTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgcagca       >  1:1409078/1‑149 (MQ=255)
                                                                                                                                           ggcgTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCaga     <  4:91257/149‑1 (MQ=255)
                                                                                                                                            gcgTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATc                                 >  2:1107106/1‑120 (MQ=255)
                                                                                                                                            gcgTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATc                                 <  1:1107106/120‑1 (MQ=255)
                                                                                                                                              gTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgc           <  2:712808/140‑1 (MQ=255)
                                                                                                                                              gTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTgc           >  1:712808/1‑140 (MQ=255)
                                                                                                                                              gTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGAc  >  4:810246/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                                 
TGCAGGGTTTTTAATCGGACGATTAGTGGGTGAAATGAGGGGTTATTTGGGGGTTACAGGTAAATTCCAGGCAGAAAAAAACCCCGCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGCGCTTTATGTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCTACAAAAATGTGCAAATTCAATAAATTGCAATTCAACTTGTAGGCCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTTGCCGTCAGTCTCAGTTAATCAGGTTACAACGATTAACCCTGCAGCAGAGAC  >  NC_000913/2001838‑2002128

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: