Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,159,354	C→T	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	95.5%	210.7 / ‑0.9	66	R323R (CGC→CGT)	mdtC	multidrug efflux system, subunit C
Reads supporting (aligned to +/- strand):  ref base C (1/2);  new base T (36/27);  total (37/29)
Fisher's exact test for biased strand distribution p-value = 5.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTC  >  NC_000913/2159258‑2159449                                                                                                 |                                                                                                cAATATTATCCAGAGGGTGGACAGCAGCCGGTCAAAATGACCGGGGTGGCGGGAAAGCAGTCCGGCGGCGATTGATCTGCAAAGTGCCCAGGATCGCTcc                                                                                              >  1:1135208/1‑100 (MQ=255) cAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcc                                                                                              >  1:620818/1‑100 (MQ=255) cAATATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGATGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTcc                                                                                              >  1:1080534/1‑100 (MQ=255)  aaTATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTccc                                                                                             >  2:1024988/1‑100 (MQ=255)  aaTATTATCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTccc                                                                                             >  2:1024974/1‑100 (MQ=255)    tattatCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTccccc                                                                                           <  2:1190299/100‑1 (MQ=255)      ttatCCAGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCccac                                                                                         <  1:201699/100‑1 (MQ=255)            aGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTcg                                                                                   >  2:1795467/1‑100 (MQ=255)            aGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTcg                                                                                   <  2:1888252/100‑1 (MQ=255)            aGACGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTcg                                                                                   >  1:804494/1‑100 (MQ=255)               cGGTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCgcgc                                                                                >  2:151956/1‑100 (MQ=255)                ggTTGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGcc                                                                               <  2:240113/100‑1 (MQ=255)                  ttGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTc                                                                             >  1:420770/1‑100 (MQ=255)                   tGACAGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCg                                                                            >  1:1758929/1‑100 (MQ=255)                    gagaGCATCCGGGCAAAAGTAGCGGAGTTGGGGGAGACCATGCCGGCGGCGATTGATCTGCAAAGTGCCGAGGATCGTTCCCCCGCGATTCGCGCCTCGc                                                                           <  1:207428/97‑1 (MQ=255)                      catcATCCGGGCAAAAGTACCGTAGTTACAGGGAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCCGGATCGTTCCCCCACCATTCGCGCCTctc                                                                           <  1:207416/95‑3 (MQ=255)                       aGCATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTgg                                                                        <  2:231660/100‑1 (MQ=255)                         cATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaa                                                                      >  1:1584230/1‑100 (MQ=255)                         cATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaa                                                                      >  2:1120781/1‑100 (MQ=255)                         cATCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTAGCTggca                                                                      >  2:1133416/1‑98 (MQ=255)                          aTCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaag                                                                     >  2:1358721/1‑100 (MQ=255)                          aTCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaag                                                                     >  1:1377151/1‑100 (MQ=255)                           tCCGGGCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGgaaga                                                                    >  1:1595386/1‑100 (MQ=255)                              gggCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGt                                                                 <  2:1692648/100‑1 (MQ=255)                                gCAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCg                                                               <  1:32933/100‑1 (MQ=255)                                 cAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGa                                                              <  1:385203/100‑1 (MQ=255)                                 cAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGa                                                              >  2:381694/1‑100 (MQ=255)                                 cAAAATTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGa                                                              >  2:287442/1‑100 (MQ=255)                                  aaaaTTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCACAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAg                                                             <  1:992242/100‑1 (MQ=255)                                   aaaTTACCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGc                                                            <  2:240671/100‑1 (MQ=255)                                        aCCGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACg                                                       <  2:1831034/100‑1 (MQ=255)                                         ccGGAGTTGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGc                                                      >  1:1630678/1‑100 (MQ=255)                                             aGTTGCAGGAACCCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGCTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGAt                                                  <  2:1383656/100‑1 (MQ=255)                                                tGCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTAt                                               <  1:446409/100‑1 (MQ=255)                                                 gCAGGAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTAt                                               >  1:1542569/1‑99 (MQ=255)                                                    ggAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCg                                           >  2:1084682/1‑100 (MQ=255)                                                    ggAAACCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCg                                           >  1:549014/1‑100 (MQ=255)                                                      aaaCCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGt                                         >  1:10355/1‑100 (MQ=255)                                                        aCCATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCCCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTgg                                       <  1:85411/100‑1 (MQ=255)                                                         ccATTCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGgc                                      >  2:860573/1‑100 (MQ=255)                                                            ttCCGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCt                                   <  2:620819/100‑1 (MQ=255)                                                              ccGGCGGCGATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTgg                                 >  2:1855829/1‑100 (MQ=255)                                                                  cggcgATTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGAt                             >  2:1651483/1‑100 (MQ=255)                                                                   ggcgATTGATCTGCAGATTGCCCAGGAGGGTTCCCCCACCATTCGCGCCTCGGTGGGAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGAt                             <  1:1370419/99‑1 (MQ=255)                                                                    gcgATTGATCTGCAAATTGCCCAGGAGCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTc                           <  1:1299377/100‑1 (MQ=255)                                                                       aTTGATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCtgg                        <  2:327246/100‑1 (MQ=255)                                                                          gATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCtggtgg                     <  2:859559/100‑1 (MQ=255)                                                                          gATCTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCtggtgg                     >  2:1257642/1‑100 (MQ=255)                                                                             cTGCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGgtgt                  >  2:1731803/1‑100 (MQ=255)                                                                               gCAAATTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGttt                >  2:41851/1‑100 (MQ=255)                                                                                 aaaTTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGttttt              >  2:859693/1‑100 (MQ=255)                                                                                 aaaTTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGttttt              <  2:1843890/100‑1 (MQ=255)                                                                                  aaTTGCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTa             <  2:4396/100‑1 (MQ=255)                                                                                   atcgCCGAGGATCGTACCCCCACCGTTGGCGCTTGGCTGGAAGATGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTa             <  1:1225658/96‑1 (MQ=255)                                                                                      gCCCGGGATCGCTCCCACACCTTTCGCGGCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTcc         <  1:240086/100‑1 (MQ=255)                                                                                      gCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTcc         >  1:1695999/1‑100 (MQ=255)                                                                                      gCCCAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTcc         <  2:1377159/100‑1 (MQ=255)                                                                                       cccAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCt        >  2:437107/1‑100 (MQ=255)                                                                                        ccAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTg       >  2:206979/1‑100 (MQ=255)                                                                                        ccAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTg       >  2:550788/1‑100 (MQ=255)                                                                                        ccAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTg       <  2:1758940/100‑1 (MQ=255)                                                                                         cAGGATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTgc      <  2:1630688/100‑1 (MQ=255)                                                                                           ggATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCt        <  1:1358713/96‑1 (MQ=255)                                                                                           ggATCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTgcgc    >  2:666231/1‑100 (MQ=255)                                                                                             aTCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTc  >  2:1509146/1‑100 (MQ=255)                                                                                             aTCGTTCCCCCACCATTCGCGCCTCGCTGGAAGAAGTCGAGCAAACGCTGATTATCTCGGTGGCGCTGGTGATTCTGGTGGTGTTTTTATTCCTGCGCTc  >  2:1716186/1‑100 (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 < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑