Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	257,794	T→C	intergenic (+23/‑35)	frsA → / → crl	fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	257,794	0	T	C	100.0%	214.5 / NA	52	intergenic (+23/‑35)	frsA/crl	fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (34/18);  total (34/18)

TGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACC  >  NC_000913/257748‑257839                                               |                                              tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:2526609/1‑50 (MQ=255) tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:2288224/1‑50 (MQ=255)  ggATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:1847648/1‑49 (MQ=255)   gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            <  1:46866/48‑1 (MQ=255)   gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:342139/49‑1 (MQ=255)   gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:172581/49‑1 (MQ=255)     tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         >  1:1086587/1‑49 (MQ=255)     tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         >  1:554126/1‑49 (MQ=255)      cGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:3515738/1‑50 (MQ=255)       gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:1367311/1‑49 (MQ=255)       gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:308486/1‑49 (MQ=255)       gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:2850875/1‑49 (MQ=255)       gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:883209/1‑49 (MQ=255)       gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       <  1:748931/49‑1 (MQ=255)         aaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAg                                    >  1:3752587/1‑50 (MQ=255)          aaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGt                                   >  1:1252820/1‑50 (MQ=255)           aaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGtt                                  >  1:739974/1‑50 (MQ=255)            aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 <  1:690934/50‑1 (MQ=255)            aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 >  1:3082676/1‑50 (MQ=255)               cTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              <  1:1735410/50‑1 (MQ=255)               cTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              <  1:1410380/50‑1 (MQ=255)                 tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            >  1:789822/1‑50 (MQ=255)                 tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            >  1:517041/1‑50 (MQ=255)                  gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            >  1:11736/1‑49 (MQ=255)                   tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcaca                          <  1:2802119/50‑1 (MQ=255)                   tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcac                           >  1:1619537/1‑49 (MQ=255)                     ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:1549409/1‑49 (MQ=255)                       aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:3116049/1‑50 (MQ=255)                        aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAgg                     <  1:164794/50‑1 (MQ=255)                         aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:1184173/1‑48 (MQ=255)                         aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGga                    <  1:103842/50‑1 (MQ=255)                         aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGga                    <  1:3173287/50‑1 (MQ=255)                           aTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGgaga                  <  1:1580898/50‑1 (MQ=255)                             ttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGgaga                  >  1:2670716/1‑48 (MQ=255)                              tGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg               >  1:3003853/1‑50 (MQ=255)                               gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg               >  1:3567793/1‑49 (MQ=255)                               gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg               <  1:896284/49‑1 (MQ=255)                                cTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGc              <  1:3239366/49‑1 (MQ=255)                                cTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCa             <  1:600227/50‑1 (MQ=255)                                 tAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCaa            >  1:1632707/1‑50 (MQ=255)                                   aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           >  1:635113/1‑49 (MQ=255)                                   aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           >  1:2294079/1‑49 (MQ=255)                                    aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa         <  1:848717/50‑1 (MQ=255)                                     ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc        >  1:3847184/1‑50 (MQ=255)                                        tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      <  1:2105999/49‑1 (MQ=255)                                        tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      >  1:2873050/1‑49 (MQ=255)                                          ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   >  1:790318/1‑50 (MQ=255)                                          ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   <  1:2766141/50‑1 (MQ=255)                                          ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   >  1:397336/1‑50 (MQ=255)                                           cAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:168637/1‑50 (MQ=255)                                           cAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:928716/1‑50 (MQ=255)                                            aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:2053275/1‑49 (MQ=255)                                               |                                              TGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACC  >  NC_000913/257748‑257839

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑