Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,332,791	0	A	C	48.8%	50.4 / 17.8	41	V161G (GTG→GGG)	basS	sensory histidine kinase in two‑component regulatory system with BasR
Reads supporting (aligned to +/- strand):  ref base A (19/2);  new base C (0/20);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 9.40e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATGGCAATGGGCG  >  NC_000913/4332647‑4332941                                                                                                                                                  |                                                                                                                                                       tGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCg                                                                                                                                                  >  1:628004/1‑151 (MQ=255)              aagaaAATGCCTGCCGGCCACCCGCAAGTGGCAGCGGCGGGGAGACGCTCTCCCTCATCTGATCACGCCGTGCCACTACCGGTGCTACATCAATGTGATGCGTTTCCGCAAGCAGTTCCAGCTGA‑AACCGCACCCCCGCCAGTg                                                                                                                                            <  1:152234/144‑1 (MQ=255)                 aaaaTGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGc                                                                                                                                    >  2:339557/1‑149 (MQ=255)                  aaaTGCCTGTCCGCCCCGCGCCAGTTGCAGCGGCGGGGAGACGCTCTCAATCTTCTGACAAAGCCGTGCCACTACGGGTGCTACATCAATGTGATGCTTTTTCGCCAGCATTTCCAGATGC‑AAACGCCCCCCCGCCAGTGGCGTTCGCAGt                                                                                                                                 <  2:70424/151‑1 (MQ=255)                     tGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCg                                                                                                                              >  2:770686/1‑151 (MQ=255)                           tCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGcgcg                                                                                                                        >  2:282078/1‑151 (MQ=255)                           ccgggCACGCCCCAGTTGCAGCAGCGGGGAGACGCTCCCCATCATCTGATCAAGCCGTGCCACAAACGGTGCTACATAAATGTGATGCTTTTTCGCCAGCAGTTCCAGATGA‑AAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTgc                                                                                                                           <  2:857562/145‑1 (MQ=255)                                  cgcgCCTTTGGCAGCAGAGGGGAGCCCCTCCCCTTCTTCTGATCAAGCCGCCCCATTAACGGTGCTACATCAATGTGTTGCTTTTTCGCCAGCGTTCCCAGAGCG‑AAACCCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTc                                                                                                                   <  1:155408/149‑1 (MQ=255)                                         gTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTaa                                                                                                           >  1:31152/1‑150 (MQ=255)                                          tggcagcaGCGGGGAGACGCTCTCCATCATCTAATCAAGCCGTCCCACTAAGGGTGCTACATAAATGTGATGCTTTTTCGCCAGCAGTCCCAGATGC‑AACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTaaa                                                                                                          <  2:361455/148‑1 (MQ=255)                                                  ggggggaccccccccccATCTTCTGATCACGCCGCCCCACTAACGGTGCTACATCATTGTGAGGCGTTTTCCCCAGCAGTCCCAGATGA‑AAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTc                                                                                                 <  1:159913/136‑1 (MQ=255)                                                     gggAGCCCCTCCCCACCATCGAACCAACCCGTGCCAGTACCGGTCCAACACCAATGTAATGCTTTTTCGCCAGCATTCCCAGATGA‑AACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTc                                                                                                 <  2:783147/148‑1 (MQ=255)                                                      ggAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGtt                                                                                              >  2:84483/1‑150 (MQ=255)                                                       gagaCGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTAt                                                                                            >  1:242665/1‑151 (MQ=255)                                                             ctctCCATCATTTTACCACCCCGTGCCACAAACGGTGTTACATCATTGTGATGTGTTTCCGCCATCAGTTCCAGATGC‑AAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGc                                                                                       <  1:107700/150‑1 (MQ=255)                                                                         ttaTCAAGCCGTCCCACTAACGGTGCTCCATAATTGTGATGTTTTTCCGCCAGCAGTTCCAGATGA‑AAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTgg                                                                                <  2:548481/143‑1 (MQ=255)                                                                          gaccAAGCCGTGCCCCTAACGGTCCTACATCAATGTGTTGCTTTTTCGCCAGCAGTCCCAGATGC‑AACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAg                                                                            <  2:242669/145‑1 (MQ=255)                                                                          gATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCg                                                                         >  2:831168/1‑151 (MQ=255)                                                                          gATAAAGCCGTGCCACAAGCGGTCTTACATCAGTGGGACGCGTTCTCGCCAGCGTTGCGAAATGC‑ACCCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAg                                                                            <  2:899459/148‑1 (MQ=255)                                                                           accAAGCCGTGCCACTAACGGTCCTACATCAATGTGATGCGTTTTCGCCGGCGTTTCAAGAGAC‑AAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCa                                                                             <  1:9109/144‑1 (MQ=255)                                                                            tCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGAc                                                                       >  2:71617/1‑151 (MQ=255)                                                                                gccggccctcTAGCGGTGCTACATAAAGGTGAGGCTTTTTCGCCAGCTGTTCAAGATGC‑AAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGa                                                                    <  1:695287/141‑1 (MQ=255)                                                                                 ccGTGCCACAAGCGGTGCAACATAAATGTGATGCGTTTCCGCAAGCAGTTCCAGATCA‑AACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGa                                                                        <  1:217991/145‑1 (MQ=255)                                                                                 ccGGGCCACTAGCGGTGCTACATCAATGTGATGCTTTTTCGCAAGCATTCCCAGATGC‑AACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCg                                                                         <  1:903761/144‑1 (MQ=255)                                                                                   gTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGAcc                                                                  >  2:566796/1‑149 (MQ=255)                                                                                           agcGGTGCTACAACAATGTGATGTTTTTCCCCCAGCTTTTCCAGAAGC‑AACCCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTa                                                        <  1:333299/149‑1 (MQ=255)                                                                                           aaCGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGttt                                                         >  1:867770/1‑150 (MQ=255)                                                                                             cGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAAc                                                      >  1:582715/1‑151 (MQ=255)                                                                                                  cTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCg                                                  >  2:315506/1‑150 (MQ=255)                                                                                                    aCATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGaa                                                >  2:570292/1‑150 (MQ=255)                                                                                                     cATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAac                                              >  2:736948/1‑151 (MQ=255)                                                                                                       tCAATGTGGTGCTTTTTCGCCAGCATTTCCAGATGC‑AACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGa                                                 <  2:628019/146‑1 (MQ=255)                                                                                                         aaTGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAaccac                                           >  1:329762/1‑150 (MQ=255)                                                                                                            gtgATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCt                                       >  1:349417/1‑151 (MQ=255)                                                                                                              gATGCTTTTTCCCCAGAATTCCAAGATCA‑AAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCtt                                      <  1:337711/150‑1 (MQ=255)                                                                                                                     tttCGCCGGCACTCCCA‑ATGCAAAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTc                               <  2:918228/150‑1 (MQ=255)                                                                                                                     tttCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCg                              >  2:7558/1‑151 (MQ=255)                                                                                                                      tccGCCAGCAGTCCGAGATGC‑AAACGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGAtt                                 <  1:477318/145‑1 (MQ=255)                                                                                                                        ccccAGCAGTCCAAGAGCC‑AAACCCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGa                             <  2:487460/147‑1 (MQ=255)                                                                                                                                      gaagC‑AACCGCCCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCtg                  <  1:387136/143‑1 (MQ=255)                                                                                                                                                 cACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATGGCAATGGGc   >  1:91363/1‑151 (MQ=255)                                                                                                                                                  aCCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATGGCAATGGGCg  >  2:743632/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                                       TGATAATTACCGGAAGAAAATGACTGTCCGGCACGCGCCAGTTGCAGCAGCTGGGAGACGCTCTCCATCATCTGATCAAGCCGTGCCACTAACGGTGCTACATCAATGTGATGCGTTTTCGCCAGCAGTTCCAGATGC‑AAACGCACCCCCGCCAGTGGCGTTCGCAGTTCGTGCGCGACGTCAGCGGTAAACAACCTTTCGTTATCCAGCGTGCTGGTCAGGCGACTGACCAGATCGTTTAACGCCGAAACCACCGCTTCGATTTCGAGGGTGGCGCTGTGAATGGCAATGGGCG  >  NC_000913/4332647‑4332941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑