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%	124.5 / NA	30	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 . (20/10);  total (20/10)

ATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGT  >  NC_000913/3658886‑3659034                                                                         |                                                                             aTTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGa                                                                     >  1:710640/1‑81 (MQ=255)             gACATAAGCATCTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGgag                                                         <  1:710586/81‑1 (MQ=255)             gACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAg                                                            >  2:710641/1‑78 (MQ=255)             gACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAg                                                            >  1:710629/1‑78 (MQ=255)             gACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGgag                                                         <  2:710585/81‑1 (MQ=255)                 tAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGc                                                     >  1:710634/1‑81 (MQ=255)                   aGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCt                                                    <  1:710588/80‑1 (MQ=255)                   aGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTa                                                   <  1:710587/81‑1 (MQ=255)                     cAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTaaa                                                 <  1:710589/81‑1 (MQ=255)                      aaCTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTaaaa                                                >  2:710625/1‑81 (MQ=255)                         tGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGa                                             >  2:710664/1‑81 (MQ=255)                                   ggctggcATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTccc                                   >  1:710653/1‑81 (MQ=255)                                      tggcATGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTg                                >  1:710652/1‑81 (MQ=255)                                          aTGACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTAt                            <  2:710590/81‑1 (MQ=255)                                            gACGAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTAtgt                          >  2:710636/1‑81 (MQ=255)                                               gAGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTa                       >  1:710639/1‑81 (MQ=255)                                                aGGGATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTAt                      >  2:710645/1‑81 (MQ=255)                                                 gggATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATc                     >  1:710644/1‑81 (MQ=255)                                                  ggATGCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATcc                    <  1:710591/81‑1 (MQ=255)                                                      gCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATccac                  >  1:710657/1‑79 (MQ=255)                                                      gCAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATccac                  >  2:710651/1‑79 (MQ=255)                                                       cAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATccacca                <  2:710592/80‑1 (MQ=255)                                                       cAGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAg               <  1:710593/81‑1 (MQ=255)                                                        aGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAg               >  2:710632/1‑80 (MQ=255)                                                        aGATGCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAg               >  2:710635/1‑80 (MQ=255)                                                            gCTGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGaa          >  2:710666/1‑81 (MQ=255)                                                              tGATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAAcc        >  1:710646/1‑81 (MQ=255)                                                               gATTTCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAAccc       >  2:710668/1‑81 (MQ=255)                                                                   tCATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTc    <  1:710594/80‑1 (MQ=255)                                                                    cATTA‑CCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGt  >  1:710615/1‑81 (MQ=255)                                                                         |                                                                             ATTTTTAGTCAGGACATAAGCAACTGAAATTGATGGCTGGCATGACGAGGGATGCAGATGCTGATTTCATTACCCCCGGTGATTACTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGT  >  NC_000913/3658886‑3659034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑