Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	1,551,980	(T)8→9	intergenic (‑337/+29)	ompN ← / ← nifJ	porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	1,551,972	1	.	T	100.0%	160.3 / NA	39	intergenic (‑329/+37)	ompN/nifJ	porin OmpN/pyruvate:ferredoxin (flavodoxin) oxidoreductase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (10/29);  total (10/29)

CCACTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑TTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAATCGG  >  NC_017635/1551923‑1552016                                                   |                                             ccACTGTTTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGc                                               >  2:1891121/1‑50 (MQ=255)  cACTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑t                                             >  1:846795/1‑50 (MQ=255)  cACTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑t                                             <  2:408153/50‑1 (MQ=255)   aCTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tt                                            <  1:533880/50‑1 (MQ=255)   aCTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tt                                            >  2:846023/1‑50 (MQ=255)    cTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttt                                           <  2:950357/50‑1 (MQ=255)    cTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttt                                           <  1:727444/50‑1 (MQ=255)       aTTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tttttt                                        >  2:1234827/1‑50 (MQ=255)       aTTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tttttt                                        >  1:1346248/1‑50 (MQ=255)       aTTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttt                                         <  2:260571/49‑1 (MQ=255)       aTTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttt                                         <  1:104818/49‑1 (MQ=255)        ttttCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttttt                                       <  1:1763121/50‑1 (MQ=255)        ttttCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttttt                                       <  2:1548235/50‑1 (MQ=255)        ttttCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttttt                                       <  2:236177/50‑1 (MQ=255)         tttCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tttttttt                                      >  2:1506999/1‑50 (MQ=255)          ttCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tttttttt                                      >  1:833283/1‑49 (MQ=255)           tCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttttttt                                     <  1:244352/49‑2 (MQ=255)           tCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttttttt                                     <  1:715625/49‑2 (MQ=255)           tCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑tttttttt                                      >  1:305760/1‑48 (MQ=255)            ccAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑ttttttttta                                    <  1:2073163/49‑3 (MQ=255)               aCATATAAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAAt                                 >  1:1620334/1‑50 (MQ=255)                 atatAAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTg                               <  2:1406584/50‑1 (MQ=255)                    taAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGa                             <  2:2027438/49‑1 (MQ=255)                    taAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGa                             <  2:1662916/49‑1 (MQ=255)                    taAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGa                             <  2:810639/49‑1 (MQ=255)                    taAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGAt                            <  2:710444/50‑1 (MQ=255)                    taAAAAGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGAt                            <  1:88637/50‑1 (MQ=255)                      aaaaGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATa                           <  1:549489/49‑1 (MQ=255)                      aaaaGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATa                           <  2:130753/49‑1 (MQ=255)                       aaaGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAAt                         <  1:1545694/50‑1 (MQ=255)                       aaaGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAAt                         <  1:2002617/50‑1 (MQ=255)                        aaGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATc                        <  2:137066/50‑1 (MQ=255)                         aGACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAAtac                       <  1:1867397/50‑3 (MQ=255)                          gACAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCt                      <  2:84739/50‑1 (MQ=255)                            cAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTa                    >  1:911511/1‑50 (MQ=255)                            cAAGCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTa                    <  1:2001655/50‑1 (MQ=255)                               gCCCGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATcc                 <  2:1032336/50‑1 (MQ=255)                                cccGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCa                <  1:1220576/50‑1 (MQ=255)                                 ccGAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATc                  >  2:802588/1‑47 (MQ=255)                                   gAACAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCagag             >  1:828498/1‑50 (MQ=255)                                    aaCAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCaggg             >  1:400944/1‑47 (MQ=255)                                    aaCAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCagag             >  1:948085/1‑49 (MQ=255)                                    aaCAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCagag             >  1:874508/1‑49 (MQ=255)                                    aaCAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCagag             >  2:1030034/1‑49 (MQ=255)                                    aaCAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGc            <  1:240899/50‑1 (MQ=255)                                      cAGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCAt          <  1:154256/50‑1 (MQ=255)                                       aGTCGTCCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCAtt         <  2:670202/50‑1 (MQ=255)                                        gtcgtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCAttt        <  2:654195/50‑1 (MQ=255)                                        gtcgtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCAttt        <  1:1708975/50‑1 (MQ=255)                                         tcgtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTa       <  1:287444/50‑1 (MQ=255)                                         tcgtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTa       <  1:981609/50‑1 (MQ=255)                                         tcgtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTa       <  2:594509/50‑1 (MQ=255)                                          cgtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTaa      >  1:1604388/1‑50 (MQ=255)                                           gtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTaa      <  2:1289506/49‑1 (MQ=255)                                           gtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAAt     <  1:407609/50‑1 (MQ=255)                                           gtcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAAt     <  2:1573487/50‑1 (MQ=255)                                            tcCGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAATc    <  1:173674/50‑1 (MQ=255)                                              cGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAATCgg  >  2:1948158/1‑50 (MQ=255)                                              cGGGCTTTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAATCg   <  2:1542688/49‑1 (MQ=39)                                                   |                                             CCACTGATTTTCCAACATATAAAAAGACAAGCCCGAACAGTCGTCCGGGC‑TTTTTTTTAGAATTGGATAATCCTTATCCAGAGCATTTAATCGG  >  NC_017635/1551923‑1552016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑