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%	351.3 / NA	85	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 (47/38);  total (47/38)

CTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACC  >  NC_000913/257747‑257839                                                |                                              cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             <  1:2171609/50‑1 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             >  1:3782624/1‑50 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             >  1:443320/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:2148529/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:2670336/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:3274464/1‑50 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           >  1:3862382/1‑49 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:1513425/49‑1 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:3049939/49‑1 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:984498/49‑1 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTa                                          <  1:720232/50‑1 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTa                                          <  1:1736462/50‑1 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         <  1:1919727/50‑1 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTa                                          >  1:3422566/1‑49 (MQ=255)      tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         >  1:1937450/1‑49 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       <  1:2291244/49‑1 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:2808544/1‑48 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:1580194/1‑48 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:623785/1‑48 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:1853510/1‑48 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:1926062/1‑48 (MQ=255)         aaaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACa                                     <  1:3023864/50‑1 (MQ=255)          aaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAg                                    >  1:4296375/1‑50 (MQ=255)           aaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGt                                   >  1:315109/1‑50 (MQ=255)             aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 >  1:3727777/1‑50 (MQ=255)             aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 <  1:3144345/50‑1 (MQ=255)              cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 >  1:4288906/1‑49 (MQ=255)              cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 >  1:1161226/1‑49 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                               <  1:2856651/50‑1 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                               <  1:2680325/50‑1 (MQ=255)                cTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:4229573/1‑50 (MQ=255)                 ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:4211444/1‑49 (MQ=255)                 ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:4326817/1‑49 (MQ=255)                 ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:3491557/1‑49 (MQ=255)                 ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:1606231/1‑49 (MQ=255)                  tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            >  1:4208421/1‑50 (MQ=255)                  tgtgTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            >  1:2660715/1‑50 (MQ=255)                   gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            <  1:3611443/49‑1 (MQ=255)                   gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            <  1:3787059/49‑1 (MQ=255)                   gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATca                            <  1:1278540/49‑1 (MQ=255)                   gtgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATc                             <  1:601667/48‑1 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcaca                          <  1:2045318/50‑1 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcaca                          <  1:2800217/50‑1 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcaca                          <  1:3679239/50‑1 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcac                           <  1:468986/49‑1 (MQ=255)                    cgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcac                           <  1:106749/48‑1 (MQ=255)                     gtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:2075447/1‑50 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaac                        <  1:3333916/50‑1 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         <  1:1671716/49‑1 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:3260394/1‑49 (MQ=255)                       tAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:3259044/1‑48 (MQ=255)                        aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:2942258/1‑50 (MQ=255)                        aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:445869/1‑50 (MQ=255)                        aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:1312977/1‑50 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAgg                     <  1:2503073/50‑1 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:487149/1‑49 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:2454238/1‑49 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:4142784/1‑48 (MQ=255)                           aaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:3131946/1‑47 (MQ=255)                           aaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:2281418/1‑47 (MQ=255)                             tttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGAt                 <  1:2960015/50‑1 (MQ=255)                             tttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGAt                 <  1:2862057/50‑1 (MQ=255)                              ttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGgaga                  >  1:107683/1‑48 (MQ=255)                               tGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg               >  1:1815665/1‑50 (MQ=255)                                gCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAg               >  1:2392207/1‑49 (MQ=255)                                 cTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGc              >  1:2000735/1‑49 (MQ=255)                                 cTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGc              <  1:4220233/49‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           <  1:2173829/49‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           <  1:4012801/49‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATg          <  1:1117691/50‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATg          <  1:1957547/50‑1 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa         <  1:284112/50‑1 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa         >  1:1612553/1‑50 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc        <  1:3950117/50‑1 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc        <  1:3437391/50‑1 (MQ=255)                                       tttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACg       >  1:1426689/1‑50 (MQ=255)                                        ttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACg       <  1:1395592/49‑1 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      >  1:1687984/1‑49 (MQ=255)                                          gCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGtt     <  1:1032026/49‑1 (MQ=255)                                          gCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTa    >  1:750460/1‑50 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   <  1:611595/50‑1 (MQ=255)                                            cAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:2784776/1‑50 (MQ=255)                                            cAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  <  1:3339134/50‑1 (MQ=255)                                             aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:2170486/1‑49 (MQ=255)                                             aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:3376490/1‑49 (MQ=255)                                                |                                              CTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACC  >  NC_000913/257747‑257839

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑