Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,658,962	(C)5→4	intergenic (+69/‑30)	gadE → / → gadF	DNA‑binding transcriptional activator GadE/small regulatory RNA GadF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,658,958	0	C	.	100.0%	160.7 / NA	38	intergenic (+65/‑34)	gadE/gadF	DNA‑binding transcriptional activator GadE/small regulatory RNA GadF
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (22/16);  total (22/16)

ACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTC  >  NC_000913/3658879‑3659032                                                                                |                                                                           acaTCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAc                                                                            <  1:643838/80‑1 (MQ=255)   aTCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAcccc                                                                         <  2:643838/81‑1 (MQ=255)        aTTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTAccccggt                                                                      <  1:643840/79‑4 (MQ=255)         tttttAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGa                                                                   <  1:643841/80‑1 (MQ=255)           tttAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTa                                                                >  2:643899/1‑81 (MQ=255)               gTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTa                                                             <  2:643841/80‑1 (MQ=255)                   ggACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAg                                                          >  1:643843/1‑79 (MQ=255)                   ggACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAg                                                          >  1:643884/1‑79 (MQ=255)                      cATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGagag                                                     <  1:643845/81‑1 (MQ=255)                      cATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGagag                                                     >  2:643909/1‑81 (MQ=255)                      cATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGagag                                                     <  1:643844/81‑1 (MQ=255)                       aTAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAgg                                                    >  1:643886/1‑81 (MQ=255)                            cAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTaaa                                               <  2:643845/81‑1 (MQ=255)                             aaCTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTaaaa                                              >  1:643887/1‑81 (MQ=255)                             aaCTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTaaaa                                              <  2:643846/81‑1 (MQ=255)                              aCTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAAc                                             <  1:643848/81‑1 (MQ=255)                               cTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACg                                            <  1:643849/81‑1 (MQ=255)                                 gAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGAc                                          >  2:643888/1‑81 (MQ=255)                                   aaTTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACtt                                        >  1:643895/1‑81 (MQ=255)                                   aaTTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACtt                                        >  2:643893/1‑81 (MQ=255)                                   aaTTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACtt                                        >  2:643892/1‑81 (MQ=255)                                    aTTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACttt                                       <  1:643850/81‑1 (MQ=255)                                    aTTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACtt                                        >  1:643892/1‑80 (MQ=255)                                        aTGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTc                                   <  2:643850/81‑1 (MQ=255)                                         tggctggcATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTcc                                  >  1:643902/1‑81 (MQ=255)                                         tggctggcATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTcc                                  >  2:643895/1‑81 (MQ=255)                                          ggctggcATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTccc                                 >  2:643889/1‑81 (MQ=255)                                              ggcATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTgg                             >  1:643899/1‑81 (MQ=255)                                                cATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTa                           <  2:643851/81‑1 (MQ=255)                                                 aTGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTAt                          <  2:643852/81‑1 (MQ=255)                                                    aCGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTAtgtg                       >  2:643905/1‑81 (MQ=255)                                                      gAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTa                     >  2:643902/1‑81 (MQ=255)                                                      gAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTa                     >  2:643916/1‑81 (MQ=255)                                                      gAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTa                     >  1:643905/1‑81 (MQ=255)                                                         ggATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATcc                  <  2:643853/81‑1 (MQ=255)                                                            tGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATccacc               <  2:643854/81‑1 (MQ=255)                                                             gCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATccac                >  1:643908/1‑79 (MQ=255)                                                              cAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATccacca              <  2:643855/80‑1 (MQ=255)                                                                  tGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAg          >  1:643897/1‑80 (MQ=255)                                                                   gCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGaa        >  1:643901/1‑81 (MQ=255)                                                                          tCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTc  <  1:643857/80‑1 (MQ=255)                                                                                |                                                                           ACATCTTATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTC  >  NC_000913/3658879‑3659032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑