Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,159,354	C→T	100%	R323R (CGC→CGT)	mdtC →	multidrug efflux system, subunit C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,159,354	0	C	T	98.6%	232.3 / ‑4.3	72	R323R (CGC→CGT)	mdtC	multidrug efflux system, subunit C
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (32/38);  total (33/39)
Fisher's exact test for biased strand distribution p-value = 4.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.23e-01

CAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTC  >  NC_000913/2159258‑2159449                                                                                                 |                                                                                                cAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcc                                                                                              >  1:163237/1‑100 (MQ=255) cAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcc                                                                                              <  1:2314117/100‑1 (MQ=255)  aaTATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTccc                                                                                             <  1:519312/100‑1 (MQ=255)  aaTATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcc                                                                                              <  2:1044493/99‑1 (MQ=255)   atatTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcccc                                                                                            >  1:899346/1‑100 (MQ=255)   atatTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcccc                                                                                            >  2:1229901/1‑100 (MQ=255)    tattatCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAACTTGCCCAGGATCGTTccccc                                                                                           <  2:1565102/100‑1 (MQ=255)      ttatCCAGACGGTTGACAGCATCCGGGCAAACTTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcccc                                                                                            <  2:2040120/97‑1 (MQ=255)        atCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCccacca                                                                                       >  2:1130419/1‑100 (MQ=255)         tCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCAt                                                                                      >  2:2216828/1‑100 (MQ=255)              aCGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTcgcg                                                                                 <  1:865038/100‑1 (MQ=255)               cGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCgcgc                                                                                >  2:1282351/1‑100 (MQ=255)               cGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCgcgc                                                                                <  1:2306118/100‑1 (MQ=255)                    gACGGCCTCCGGGCAACATTACGGGAGTTGTAGGAAACCATTCCGGGGGCGATTGGTCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCg                                                                            <  2:478753/99‑1 (MQ=255)                    gACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGc                                                                           >  2:63467/1‑100 (MQ=255)                     aCAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCTCCATTCGCGCCTCGCt                                                                          <  1:1195849/100‑1 (MQ=255)                     aCAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCt                                                                          >  1:1922668/1‑100 (MQ=255)                     aCAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCt                                                                          <  1:133418/100‑1 (MQ=255)                      cAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTg                                                                         <  2:2468457/100‑1 (MQ=255)                      cAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTg                                                                         <  1:1011408/100‑1 (MQ=255)                       aGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTgg                                                                        <  1:2057085/100‑1 (MQ=255)                        gCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGga                                                                       >  2:1998761/1‑100 (MQ=255)                          aTCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaag                                                                     >  2:1624737/1‑100 (MQ=255)                          aTCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaag                                                                     <  1:592049/100‑1 (MQ=255)                          aTCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaag                                                                     <  1:641161/100‑1 (MQ=255)                           tCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaaga                                                                    >  1:527907/1‑100 (MQ=255)                           tCCGGGCAAAAGTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaag                                                                     <  2:2409696/99‑1 (MQ=255)                                gCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGACGAAGTCg                                                               >  2:2547929/1‑100 (MQ=255)                                gCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCg                                                               >  2:985303/1‑100 (MQ=255)                                 cAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGa                                                              <  1:1282359/100‑1 (MQ=255)                                 cAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGa                                                              >  2:229028/1‑100 (MQ=255)                                  aaaaTTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAg                                                             <  2:213018/100‑1 (MQ=255)                                       tACCGGAGTTGCAGGAAACCATTCCGTCGGCGTTTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAAc                                                        <  2:631918/100‑1 (MQ=255)                                       tACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAAc                                                        <  2:631941/100‑1 (MQ=255)                                        aCCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCTCTGGAAGAAGTCGAGCAAACg                                                       <  2:1228993/100‑1 (MQ=255)                                         ccGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGc                                                      <  1:689552/100‑1 (MQ=255)                                         ccGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGc                                                      >  2:2518809/1‑100 (MQ=255)                                           ggAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTg                                                    <  2:2472142/100‑1 (MQ=255)                                           ggAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTACAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTg                                                    <  2:1234656/100‑1 (MQ=255)                                            gAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGa                                                   <  1:2026405/100‑1 (MQ=255)                                             aGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGAt                                                  <  2:262071/100‑1 (MQ=255)                                                tGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTAt                                               >  2:164172/1‑100 (MQ=255)                                                  cAGGAAACCATTCAGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTAtct                                             >  1:1742225/1‑100 (MQ=255)                                                    ggAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCg                                           >  2:2086912/1‑100 (MQ=255)                                                    ggAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCg                                           <  1:1576128/100‑1 (MQ=255)                                                    ggAAACCATTCCGGCGGCAATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCg                                           <  2:834652/100‑1 (MQ=255)                                                      aaaCCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGt                                         >  2:1985927/1‑100 (MQ=255)                                                        aCCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTgg                                       <  1:596840/100‑1 (MQ=255)                                                         ccATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGgc                                      >  1:965913/1‑100 (MQ=255)                                                          cATTCCGGCGGCAATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGgcg                                     >  1:1688448/1‑100 (MQ=255)                                                           aTTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGgcgc                                    >  1:1337609/1‑100 (MQ=255)                                                              ccGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTgg                                       >  2:2313599/1‑94 (MQ=255)                                                              ccGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTgg                                 >  2:2421841/1‑100 (MQ=255)                                                               cggcggCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGt                                <  1:1797644/100‑1 (MQ=255)                                                                ggcggcGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGACTCGCGGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGt                                <  2:899338/99‑1 (MQ=255)                                                                  cggcgATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGgcggcggt                                >  2:799467/1‑92 (MQ=255)                                                                  cggcgATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTg                               <  2:1951844/98‑1 (MQ=255)                                                                  cggcgATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTCGTg                               >  2:2088663/1‑98 (MQ=255)                                                                    gcgGTTGATCTGCAAATTTCCTATGTTCGTTCCCCCACCATTCGCGCCTCGCTGGTCGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTg                               <  2:183775/96‑1 (MQ=255)                                                                     cgATTTATCAGCAAATCGCCCGGGAGCGGGGCGCCACCCTTCGTGCCCCGCTGGGAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGAt                             <  2:1066247/97‑1 (MQ=255)                                                                     cgATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCCGGTGATTCt                          >  2:1471973/1‑100 (MQ=255)                                                                          gATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCggtggtagtactg                         >  2:2222491/1‑89 (MQ=255)                                                                             cTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGgtggtg                   >  2:1978210/1‑99 (MQ=255)                                                                                cAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGtttt               <  1:1998775/100‑1 (MQ=255)                                                                                  aaTTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGtttt               <  1:2492409/98‑1 (MQ=255)                                                                                  aaTTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTa             >  2:191799/1‑100 (MQ=255)                                                                                   aTTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTAt            <  1:2466990/100‑1 (MQ=255)                                                                                    ttGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTAtt           <  1:690927/100‑1 (MQ=255)                                                                                     tGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGACGTCGAGCAAACGCTGATTATCTCGGTGGCGTTGGTGATTCTGGTGGTGTTTTTAtt           >  1:2460021/1‑99 (MQ=255)                                                                                      gCCGAGGATCGTTCACCCACGATGCGGGCGTTGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTAtt           <  2:2095712/98‑1 (MQ=255)                                                                                       cccAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCt        >  1:573045/1‑100 (MQ=255)                                                                                             aTCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTc  >  1:1528972/1‑100 (MQ=255)                                                                                                 |                                                                                                CAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTC  >  NC_000913/2159258‑2159449

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑