Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,880,357	A→C	7.9%	N731T (AAC→ACC)	mexF →	multidrug RND transporter MexF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,880,357	0	A	C	7.9%	152.4 / 2.1	50	N731T (AAC→ACC)	mexF	multidrug RND transporter MexF
Reads supporting (aligned to +/- strand):  ref base A (23/23);  new base C (2/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

GCCTGGGCACGATTGGCGGGTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAACGACTTCAACCGCTTTGGCCGCACTTACCAGGTCAAC  >  NC_002947/3880210‑3880505                                                                                                                                                    |                                                                                                                                                        gCCTGGGCACGATTGGCGGGTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAAc                                                                                                                                                        <  4:26343/149‑1 (MQ=255)      ggCACGATTGGCGGGTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGGTACGAAGCGCTGGACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGcc                                                                                                                                                   <  6:203939/149‑1 (MQ=255)                  gggTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATgc                                                                                                                                       >  3:120027/1‑149 (MQ=255)                   ggTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCACCGTGCCACAAGTCGATgcc                                                                                                                                      >  5:58326/1‑149 (MQ=255)                   ggTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCACCGTGCCACAAGTCGATgcc                                                                                                                                      >  5:52667/1‑149 (MQ=255)                        cGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCAt                                                                                                                              <  8:180446/149‑1 (MQ=255)                        cGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCAt                                                                                                                              >  2:133650/1‑149 (MQ=255)                              cAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCg                                                                                                                        >  2:253/1‑149 (MQ=255)                               aaaTCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCgg                                                                                                                       <  1:133650/149‑1 (MQ=255)                                aaTCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCgg                                                                                                                       >  1:344501/1‑148 (MQ=255)                                    gAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGaaaa                                                                                                                  <  2:344501/149‑1 (MQ=255)                                    gAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACAAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGaa                                                                                                                    >  2:129467/1‑147 (MQ=255)                                           gTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGcc                                                                                                              >  5:319673/1‑146 (MQ=255)                                              gCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAg                                                                                                                 >  4:323906/1‑140 (MQ=255)                                              gCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAg                                                                                                                 <  3:323906/140‑1 (MQ=255)                                               cAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATgcc‑‑‑g                                                                                                                                  >  1:2813/1‑122 (MQ=255)                                               cAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATgcc‑‑‑g                                                                                                                                  <  2:2813/122‑1 (MQ=255)                                               cAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGAcc                                                                                                        >  3:98540/1‑148 (MQ=255)                                                  ccTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTTCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCAc                                                                                                     <  6:360412/148‑1 (MQ=255)                                                  ccTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCAc                                                                                                     >  5:360412/1‑148 (MQ=255)                                                      ggTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGgt                                                                                                  <  4:120027/147‑1 (MQ=255)                                                           cGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGa                                                                                           <  4:98540/149‑1 (MQ=255)                                                            gAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAgg                                                                                                                <  2:291736/127‑1 (MQ=255)                                                            gAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAgg                                                                                                                >  1:291736/1‑127 (MQ=255)                                                            gAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGAt                                                                                          >  4:52986/1‑149 (MQ=255)                                                               gcgcTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCACCGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCAc                                                                                       <  6:58326/149‑1 (MQ=255)                                                               gcgcTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCACCGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCAc                                                                                       <  6:52667/149‑1 (MQ=255)                                                                 gcTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGGTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCTGTAAAAGGGCAAGACCCAATGTGTGGCGATCACCg                                                                                     <  4:259434/149‑1 (MQ=255)                                                                      aCAAGGAAACCCAGAACATCATCGCCAAGAGCCCCAACGTCCCAGAGCTGGCAGGCCAGTTCACCAGCAACCAGGTCAACGAGCCACAAGTAGAAGCCGTGGCGGCCGCCCCGGAAAAGGCCAAGAACCACGTTGTGGCGAGCAACGa                                                                                    >  1:126472/1‑148 (MQ=255)                                                                        aaGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCtt                                                                              >  5:104447/1‑149 (MQ=255)                                                                         aGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTc                                                                             <  1:129467/149‑1 (MQ=255)                                                                                ccAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACAccc                                                                      >  6:255073/1‑149 (MQ=255)                                                                                   gAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACAAGCTACCAGGTCAACGTGCCACAAGTCGATGCA‑‑‑GCCATCGACCGGGAAAAGGCCAAGACGCAAGGTGTGGCGATCACAGAAATCTTAGacacaatg                                                                    >  8:178122/1‑144 (MQ=255)                                                                                     aCATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAg                                                                 <  3:270162/149‑1 (MQ=255)                                                                                        tcatcGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGtt                                                              >  2:205486/1‑149 (MQ=255)                                                                                           tcGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTAc                                                           <  3:52986/149‑1 (MQ=255)                                                                                              ccAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAg                                                                 <  1:362794/140‑1 (MQ=255)                                                                                              ccAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAg                                                                 >  2:362794/1‑140 (MQ=255)                                                                                                       acaACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTg                                               >  3:108710/1‑149 (MQ=255)                                                                                                            gTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCCACATCTTCGACACCCTGCAGGTTTACCTgg                                                       <  4:329844/136‑1 (MQ=255)                                                                                                            gTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCCACATCTTCGACACCCTGCAGGTTTACCTgg                                                       >  3:329844/1‑136 (MQ=255)                                                                                                            gTCCCAGAGCTGGAAGGCCTTTTCACCAGCTACAATGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAACGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTacac                                          <  7:178122/149‑1 (MQ=255)                                                                                                                    gCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAACGAc                                   <  6:104447/148‑1 (MQ=255)                                                                                                                        gCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTc                                                                             <  2:137216/102‑1 (MQ=255)                                                                                                                        gCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTc                                                                             >  1:137216/1‑102 (MQ=255)                                                                                                                              cTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTaca                                           <  6:61908/130‑1 (MQ=255)                                                                                                                              cTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCAACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTaca                                           >  5:61908/1‑130 (MQ=255)                                                                                                                               tGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAAc                                      >  1:75265/1‑134 (MQ=255)                                                                                                                               tGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAAc                                      <  2:75265/134‑1 (MQ=255)                                                                                                                                 ttCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAACGACTTCAACCGCTTTg                      <  4:108710/148‑1 (MQ=255)                                                                                                                                                    aCGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAACGACTTCAACCGCTTTGGCCGCACTTACCAGGTCAAc  <  6:91485/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                        GCCTGGGCACGATTGGCGGGTTCCGTCTGCAAATCGAAGACCGTGGCAACCTGGGTTACGAAGCGCTGTACAAGGAAACCCAGAACATCATCGCCAAGAGCCACAACGTCCCAGAGCTGGCAGGCCTGTTCACCAGCTACCAGGTCAACGTGCCACAAGTCGATGCC‑‑‑GCCATCGACCGGGAAAAGGCCAAGACCCACGGTGTGGCGATCACCGACATCTTCGACACCCTGCAGGTTTACCTGGGCTCGCTGTACACCAACGACTTCAACCGCTTTGGCCGCACTTACCAGGTCAAC  >  NC_002947/3880210‑3880505

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑