Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,935,640	T→C	12.1%	Q332R (CAG→CGG)	flhA ←	flagellar export pore protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,935,640	0	T	C	12.1%	80.6 / 2.5	33	Q332R (CAG→CGG)	flhA	flagellar export pore protein
Reads supporting (aligned to +/- strand):  ref base T (13/16);  new base C (2/2);  total (15/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01

GATCAGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGCGAATCGAACATCTGCCGA  >  NC_002947/4935492‑4935789                                                                                                                                                       |                                                                                                                                                      gATCAGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCctgctg                                                                                                                                                      <  2:110238/150‑1 (MQ=255)  aTCAGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGATGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCctgctgc                                                                                                                                                     >  2:231638/1‑150 (MQ=255)    cAGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCctgctgctg                                                                                                                                                   <  2:597372/150‑1 (MQ=255)     aGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCtgctgctgc                                                                                                                                                  <  2:745232/150‑1 (MQ=255)     aGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCtgctgctgc                                                                                                                                                  <  2:139669/150‑1 (MQ=255)      gCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTgctgctgct                                                                                                                                                 >  1:417685/1‑150 (MQ=255)      gCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTgctgctgct                                                                                                                                                 >  2:585067/1‑150 (MQ=255)        cGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGcttc                                                                                                                                               <  1:659857/150‑1 (MQ=255)           tAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGATGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCttcttc                                                                                                                                            <  1:231638/150‑1 (MQ=255)           tAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTACCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCttcttc                                                                                                                                            <  2:413588/150‑1 (MQ=255)             gCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCca                                                                                                                                          <  1:721460/150‑1 (MQ=255)                                aTGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGccgccg                                                                                                                       >  2:93230/1‑150 (MQ=255)                                  gTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGctt                                                                                                                                                >  1:600030/1‑123 (MQ=255)                                  gTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGctt                                                                                                                                                <  2:600030/123‑1 (MQ=255)                                     gATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGgccgc                                                                                                                  >  2:707274/1‑150 (MQ=255)                                             tGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGc                                                                                                          <  2:297302/150‑1 (MQ=255)                                              gACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGAGCCACTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGcc                                                                                                         >  1:466406/1‑150 (MQ=255)                                                cgtcgtCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGa                                                                                                       <  2:397525/150‑1 (MQ=255)                                                  tcgtcCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAgg                                                                                                     <  2:429653/150‑1 (MQ=255)                                                       ccAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGTAGGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGGGGCTGAg                                                                                                >  1:361470/1‑150 (MQ=255)                                                       ccAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCtgctgctgc                                                                                                                                                  >  1:219049/1‑100 (MQ=255)                                                       ccAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCtgctgctgc                                                                                                                                                  <  2:219049/100‑1 (MQ=255)                                                             cAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGc                                                                                          >  2:734772/1‑150 (MQ=255)                                                                     tGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTGCCCCTACACGACG‑CTCTT‑CTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCg                                                                                  <  2:583807/150‑1 (MQ=255)                                                                            cAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGcc                                                                           >  2:41483/1‑150 (MQ=255)                                                                                          gctaGGGCAGCCGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCa                                                             >  2:672843/4‑150 (MQ=255)                                                                                               ggCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCCGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACg                                                        >  2:389796/1‑150 (MQ=255)                                                                                                    cagGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCATTGACCTTGGACTGCTGCTGATTCTTCCACACCAGGTCGGCTCCGCCGGCCGCCATCCGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCCCCAACCCCATGACGatcat                                                   >  2:43060/1‑150 (MQ=255)                                                                                                      ggTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGAtcatca                                                 <  1:110359/150‑1 (MQ=255)                                                                                                                tgACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGaa                                                                                             >  2:534760/1‑98 (MQ=255)                                                                                                                tgACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGaa                                                                                             <  1:534760/98‑1 (MQ=255)                                                                                                                  aCGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCCGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGa                                       >  2:557221/1‑150 (MQ=255)                                                                                                                         gcCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGcc                                <  1:585067/150‑1 (MQ=255)                                                                                                                          ccTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGc                                                                            >  1:72760/1‑105 (MQ=255)                                                                                                                          ccTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGc                                                                            <  2:72760/105‑1 (MQ=255)                                                                                                                                 cTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGGCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCtt                        >  2:513101/1‑150 (MQ=255)                                                                                                                                 cTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCTTGACGATCATCAACGCGCCAGACACCGCCAGGGCCtt                        <  1:608279/150‑1 (MQ=255)                                                                                                                                  tGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTg                       <  2:466406/150‑1 (MQ=255)                                                                                                                                     gCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGc                    <  1:707274/150‑1 (MQ=255)                                                                                                                                     gCTTTGACCTTGGCCTGCCGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGc                    <  1:557221/150‑1 (MQ=255)                                                                                                                                       tttGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGCGa                  >  2:751288/1‑150 (MQ=255)                                                                                                                                       tttGACCTTGGCCTGCCGCTGCTTCGTCCACACGAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGGTCAGAAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGCGa                  <  1:389796/150‑1 (MQ=255)                                                                                                                                                       tgctgctTCTTCCCCACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCGGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGCGAATCGAACATCTGCCGa  <  2:315571/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                      GATCAGCCGATAGCCGACTTCCAGGCCGATCATGTCGATGGGGGTGACGTCGTCCCAACCCAGCTCCTTGGTTTCCAGCGCGCGCTGTGGCGAGGGCAGCAGGTCCTG‑‑CTGACGCTGCGCCTCTTGCTGGGCTTTGACCTTGGCCTGCTGCTGCTTCTTCCACACCAGGTAGGCGCCGCCGGCCGCCATCAGGCCGAGGCTGAGGAAGGCAATGTGCGGCATGCCCGGCACCAGCCCCATGACGATCATCAACGCGCCAGACACCGCCAGGGCCTTGGGCGAATCGAACATCTGCCGA  >  NC_002947/4935492‑4935789

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑