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%	278.7 / NA	67	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 (41/26);  total (41/26)

CTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCG  >  NC_000913/257747‑257840                                                |                                               cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                              >  1:2882830/1‑50 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                              <  1:1642369/50‑1 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                              <  1:1297426/50‑1 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                              >  1:3694925/1‑50 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                             <  1:3591733/48‑1 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                          <  1:4366053/50‑1 (MQ=255)      tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                          >  1:2138471/1‑49 (MQ=255)       cGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                        >  1:736492/1‑50 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                        >  1:3168691/1‑49 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAAc                                       <  1:3849518/50‑1 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                        >  1:1271393/1‑48 (MQ=255)          aaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAg                                     <  1:1707870/50‑1 (MQ=255)          aaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAg                                     >  1:2003680/1‑50 (MQ=255)           aaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGt                                    >  1:372232/1‑50 (MQ=255)           aaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGt                                    >  1:4396485/1‑50 (MQ=255)            aaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGtt                                   <  1:274978/50‑1 (MQ=255)             aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                  >  1:4130387/1‑50 (MQ=255)             aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                  <  1:4348587/50‑1 (MQ=255)             aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                  >  1:2982116/1‑50 (MQ=255)              cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                  >  1:3783977/1‑49 (MQ=255)              cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                  >  1:3912326/1‑49 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                                >  1:4095328/1‑50 (MQ=255)                   gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                             >  1:1966452/1‑49 (MQ=255)                   gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                             >  1:2969807/1‑49 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcaca                           <  1:1794669/50‑1 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcac                            >  1:2952258/1‑49 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcac                            <  1:5023366/49‑1 (MQ=255)                     gtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                          >  1:4282951/1‑50 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                          <  1:3370326/49‑1 (MQ=255)                       tAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                          >  1:4047235/1‑48 (MQ=255)                       tAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                          >  1:4293086/1‑48 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAgg                      <  1:3061090/50‑1 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAgg                      <  1:1552850/50‑1 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:1530688/1‑49 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:3286923/1‑49 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:1615649/1‑49 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       <  1:4283380/49‑1 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:2936196/1‑48 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:3436626/1‑48 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:3174788/1‑48 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:1984177/1‑48 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGga                     <  1:1417296/50‑1 (MQ=255)                           aaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:1839020/1‑47 (MQ=255)                           aaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:3795510/1‑47 (MQ=255)                           aaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                       >  1:799768/1‑47 (MQ=255)                              ttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGgaga                   >  1:3783889/1‑48 (MQ=255)                                gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg                >  1:2034556/1‑49 (MQ=255)                                gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg                >  1:1265731/1‑49 (MQ=255)                                gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg                <  1:1022111/49‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt            >  1:760830/1‑49 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt            >  1:877718/1‑49 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt            >  1:3363634/1‑49 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATg           <  1:3525407/50‑1 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa          <  1:3321562/50‑1 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa          <  1:2127574/50‑1 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa          >  1:1444599/1‑50 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc         >  1:4100503/1‑50 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc         <  1:3707532/50‑1 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc         >  1:4603573/1‑50 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc         <  1:117626/50‑1 (MQ=255)                                        ttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACg        <  1:4899033/49‑1 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt       >  1:399159/1‑49 (MQ=255)                                          gCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGtt      <  1:1092812/49‑1 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTa     <  1:1738163/49‑1 (MQ=255)                                            cAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc   <  1:3140373/50‑1 (MQ=255)                                             aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc   >  1:3118017/1‑49 (MQ=255)                                             aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCg  <  1:871027/50‑1 (MQ=255)                                                |                                               CTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACCG  >  NC_000913/257747‑257840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑