Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,794,436	G→C	8.3%	E552Q (GAG→CAG) ‡	bamA‑I →	outer membrane protein assembly factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,794,436	0	G	C	8.3%	140.3 / 5.0	48	E552Q (GAG→CAG) ‡	bamA‑I	outer membrane protein assembly factor
Reads supporting (aligned to +/- strand):  ref base G (22/22);  new base C (2/2);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.32e-01

AGCTATGCGGTGGACAGCTACGGTGCCGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTGTCGTTCTT  >  NC_002947/1794292‑1794581                                                                                                                                                  |                                                                                                                                                  aGCTATGCGGTGGACTGCTACGGTGCCGGCGGCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCgagga                                                                                                                                               <  2:78351/149‑1 (MQ=255)   cTATGCGGGTGACAGCTACGGTGCCGGCGTCATCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAATATCAACGACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCgaggag                                                                                                                                              <  1:69813/149‑1 (MQ=25)         ggTGGACAGCTACGGTGCCGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCCTCGAGGAAgtcg                                                                                                                                       <  4:150080/149‑4 (MQ=255)                    aCGGTGCCGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCt                                                                                                                             >  4:270983/1‑148 (MQ=255)                     cGGTGCCGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGa                                                                                                                           <  1:160660/149‑1 (MQ=255)                     cGGTGCCGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGa                                                                                                                           <  5:240548/149‑1 (MQ=255)                          ccGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGTTGTCACCTTCCtcctcga                                                                                                                       <  3:48838/148‑7 (MQ=37)                           cGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTc                                                                                                                      >  8:129980/1‑148 (MQ=255)                                   gCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAg                                                                                                                   >  4:94913/1‑143 (MQ=255)                                   gCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAg                                                                                                                   <  3:94913/143‑1 (MQ=255)                                             cccGATCAGCGAAACCTAGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGt                                                                                                   >  5:83525/1‑149 (MQ=255)                                                  tCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAg                                                                                              >  5:20414/1‑149 (MQ=255)                                                  tCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAg                                                                                              <  3:147864/149‑1 (MQ=255)                                                    aGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTc                                                                                            <  5:270119/149‑1 (MQ=255)                                                     gCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTc                                                                                            >  3:272656/1‑148 (MQ=255)                                                         aaCCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGGGGAAGGTGACAACTTCCTGAACTTCAAg                                                                                                                   >  1:162267/1‑121 (MQ=255)                                                         aaCCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGGGGAAGGTGACAACTTCCTGAACTTCAAg                                                                                                                   <  2:162267/121‑1 (MQ=255)                                                           ccTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTg                                                                                                     <  3:240461/133‑1 (MQ=255)                                                           ccTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTg                                                                                                     >  4:240461/1‑133 (MQ=255)                                                             tCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGaa                                                                                   >  6:226136/1‑149 (MQ=255)                                                               gcgcCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGaa                                                                                   <  4:82314/147‑1 (MQ=255)                                                                      aCCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGc                                                                            <  6:83525/147‑1 (MQ=255)                                                                        cTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTAc                                                                        >  1:272750/1‑149 (MQ=255)                                                                           cGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTgg                                                                     <  1:268901/149‑1 (MQ=255)                                                                            ggCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGc                                                                    >  1:177731/1‑149 (MQ=255)                                                                              ccTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACAGTTGACGAGATCTTCGACTTCCTCGAGGAGCAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCa                                                                  >  5:227050/1‑149 (MQ=255)                                                                                                cAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTCCTGGCCACCCGTGGTCACTCGcg                                                  >  2:197202/1‑146 (MQ=255)                                                                                                   gATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGcc                                             <  2:272750/149‑1 (MQ=255)                                                                                                      cAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGa                                          >  5:315388/1‑149 (MQ=255)                                                                                                      cAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGa                                          >  3:7607/1‑149 (MQ=255)                                                                                                       aa‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGAc                                         >  3:250283/1‑149 (MQ=255)                                                                                                       aa‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGAc                                         <  5:226136/149‑1 (MQ=255)                                                                                                            ccGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTg                                     <  6:20414/149‑1 (MQ=255)                                                                                                             cGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTgg                                    >  4:274576/1‑149 (MQ=255)                                                                                                                    tACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCAc                             <  4:7607/149‑1 (MQ=255)                                                                                                                             gACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCgg                     <  4:272656/148‑1 (MQ=255)                                                                                                                              aCGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCgg                     <  4:53976/147‑1 (MQ=255)                                                                                                                              aCGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCgg                     >  3:53976/1‑147 (MQ=255)                                                                                                                                        cGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTg          <  6:315388/148‑1 (MQ=255)                                                                                                                                        cGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTg          <  2:177731/148‑1 (MQ=255)                                                                                                                                         accTTCCTCCTCGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCg                      <  4:55599/133‑1 (MQ=255)                                                                                                                                         accTTCCTCCTCGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCg                      >  3:55599/3‑135 (MQ=255)                                                                                                                                         accTTCCTCCTCGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTGTc        >  6:315843/3‑149 (MQ=255)                                                                                                                                          aCTTCCTCGAGGAGGAAGGTGTCAACTTGCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAATGCGTACTGGCCACGCGTGGTCACTCGCAATGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTg          <  7:286266/146‑1 (MQ=255)                                                                                                                                          aCTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTGTCg       <  3:274576/149‑1 (MQ=255)                                                                                                                                          aCTTCCTCGACGAGGAAGCTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTTGTCCGAGTCGACCCTGAACAAAGCCGTACTGGCAACCCGTGCTCACTCGCAAAGCCTGAACCGCGAGTCCAACGTACCGGGCATCAACCTg          >  8:286266/1‑146 (MQ=255)                                                                                                                                           cTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTGTCGt      >  7:256120/1‑149 (MQ=255)                                                                                                                                                tCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGa                                   <  4:245236/115‑1 (MQ=255)                                                                                                                                                tCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGa                                   >  3:245236/1‑115 (MQ=255)                                                                                                                                                tCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTCTCGttctt  >  7:81702/1‑148 (MQ=255)                                                                                                                                                  |                                                                                                                                                  AGCTATGCGGTGGACAGCTACGGTGCCGGCGTCAGCCTGGGCTACCCGATCAGCGAAACCTCGCGCCTGACCTACGGCCTGAGCGTGCAGCAGGACAAGATCAA‑GACCGGCAAATACACCGTTGACGAGATCTTCGACTTCCTCGAGGAGGAAGGTGACAACTTCCTGAACTTCAAGGCCTCGATCGGCTGGTCCGAGTCGACCCTGAACAAAGGCGTACTGGCCACCCGTGGTCACTCGCAAAGCCTGACCCTGGAGTCCACCGTTCCGGGCAGCGACCTGTCGTTCTT  >  NC_002947/1794292‑1794581

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑