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%	331.9 / NA	82	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 (48/34);  total (48/34)

CTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACC  >  NC_000913/257747‑257839                                                |                                              cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             <  1:5030733/50‑1 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             <  1:597804/50‑1 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             <  1:2430152/50‑1 (MQ=255) cTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTg                                             >  1:2289103/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:5340791/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:334122/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:3011424/1‑50 (MQ=255)  tGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTgg                                            >  1:1776698/1‑50 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:4896774/49‑1 (MQ=255)    gATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGt                                           <  1:6035149/49‑1 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         <  1:90542/50‑1 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         <  1:25229/50‑1 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTa                                          >  1:2787558/1‑49 (MQ=255)     aTCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTa                                          >  1:1408211/1‑49 (MQ=255)      tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaa                                        <  1:4992463/50‑1 (MQ=255)      tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaa                                        <  1:6018413/50‑1 (MQ=255)      tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         >  1:1416369/1‑49 (MQ=255)      tCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaa                                         >  1:2540659/1‑49 (MQ=255)       cGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:2267946/1‑50 (MQ=255)       cGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:3198302/1‑50 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       <  1:4279507/49‑1 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:1880235/1‑49 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:825655/1‑49 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTaaaa                                       >  1:2401673/1‑49 (MQ=255)        gAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAAc                                      <  1:4230524/50‑1 (MQ=255)          aaaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAg                                    >  1:6334549/1‑50 (MQ=255)           aaaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGt                                   <  1:203232/50‑1 (MQ=255)            aaCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGtt                                  <  1:5335714/50‑1 (MQ=255)             aCGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTg                                 <  1:897477/50‑1 (MQ=255)              cGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGc                                <  1:382980/50‑1 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                               >  1:6215675/1‑50 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                               >  1:687678/1‑50 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                               <  1:111640/50‑1 (MQ=255)               gCTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCa                               >  1:4511854/1‑50 (MQ=255)                cTTGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:2608178/1‑50 (MQ=255)                 ttGTGTTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCAt                              >  1:1107509/1‑49 (MQ=255)                    tgtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATcac                           >  1:659077/1‑49 (MQ=255)                     gtTAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:2714820/1‑50 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaac                        <  1:4310511/50‑1 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaac                        <  1:4496779/50‑1 (MQ=255)                      ttAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:4957688/1‑49 (MQ=255)                       tAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:955441/1‑48 (MQ=255)                       tAAAAATTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaa                         >  1:1826817/1‑48 (MQ=255)                        aaaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCacaaca                       <  1:2911900/49‑1 (MQ=255)                         aaaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAgg                     <  1:1376170/50‑1 (MQ=255)                          aaaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:2725097/1‑48 (MQ=255)                           aaTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:2548068/1‑47 (MQ=255)                            aTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:4170544/1‑46 (MQ=255)                            aTTTGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAg                      >  1:1469581/1‑46 (MQ=255)                             tttGCTAAATTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGgaga                  >  1:4957372/1‑49 (MQ=255)                                   aaaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           >  1:3908336/1‑50 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCaa            <  1:2363575/48‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           >  1:5651452/1‑49 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAAt           <  1:1030949/49‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATg          <  1:2996987/50‑1 (MQ=255)                                    aaTTTTGCCAATCTGGTAAAACAGTTGCATCAAAACAGGAGATAGCAAt           <  1:3035346/49‑1 (MQ=38)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa         >  1:3463926/1‑50 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa         >  1:766071/1‑50 (MQ=255)                                     aTTTTGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGa         <  1:682266/50‑1 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc        <  1:1688246/50‑1 (MQ=255)                                      ttttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGAc        <  1:3169639/50‑1 (MQ=255)                                       tttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACg       >  1:644238/1‑50 (MQ=255)                                        ttGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACg       <  1:1347090/49‑1 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      <  1:52637/49‑1 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      >  1:1166008/1‑49 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      <  1:176763/49‑1 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      >  1:3232713/1‑49 (MQ=255)                                         tGCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGt      >  1:3068741/1‑49 (MQ=255)                                          gCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGtt     <  1:5332226/49‑1 (MQ=255)                                          gCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTa    >  1:2829172/1‑50 (MQ=255)                                          gCCAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTa    >  1:3546740/1‑50 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTa    <  1:6273543/49‑1 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTa    <  1:6109841/49‑1 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   >  1:2259216/1‑50 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   >  1:3534295/1‑50 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   >  1:4480390/1‑50 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   >  1:1203774/1‑50 (MQ=255)                                           ccAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAc   <  1:4795169/50‑1 (MQ=255)                                            cAATCTGGTAAAACAGTTGCATCACAACAGGAGCTAGCAATGACGTTAcc  >  1:3328976/1‑50 (MQ=39)                                            cAATCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:71870/1‑50 (MQ=255)                                             aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:692657/1‑49 (MQ=255)                                             aaTCTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTAcc  >  1:1082251/1‑49 (MQ=255)                                                |                                              CTGGATCGAAAAACGCTTGTGTTAAAAATTTGCTAAATTTTGCCAATTTGGTAAAACAGTTGCATCACAACAGGAGATAGCAATGACGTTACC  >  NC_000913/257747‑257839

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑