Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	3,213,568	C→T	intergenic (+24/+55)	rpoD → / ← ygjF	RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,213,568	0	C	T	100.0%	119.5 / NA	38	intergenic (+24/+55)	rpoD/ygjF	RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (13/25);  total (13/25)

TTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTA  >  W3110S.gb/3213511‑3213625                                                          |                                                          ttCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTAtgccg                                                       <  1:3312876/62‑1 (MQ=255) ttCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTAtgccg                                                       <  1:4226174/62‑1 (MQ=255) ttCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTAtgccg                                                       <  1:560584/62‑1 (MQ=255) ttCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTAtgccg                                                       <  1:2047181/62‑1 (MQ=255) ttCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTAtgccg                                                       <  1:2140921/62‑1 (MQ=255)     gAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCAc                                                    <  1:1189468/61‑1 (MQ=255)     gAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCAc                                                    <  1:46467/61‑1 (MQ=255)     gAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCAc                                                    <  1:2945951/61‑1 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGc                                               >  1:3761069/1‑61 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGc                                               >  1:3911021/1‑61 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGc                                               >  1:3180580/1‑61 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGc                                               >  1:1325330/1‑61 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGc                                               >  1:1481834/1‑61 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCa                                              <  1:249372/62‑1 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCa                                              <  1:1625927/62‑1 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCa                                              <  1:4439987/62‑1 (MQ=255)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACACgg                                                >  1:4240652/1‑60 (MQ=38)          gctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACACGGc                                               >  1:259078/1‑61 (MQ=255)           ctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCAc                                                    <  1:1935668/55‑1 (MQ=255)           ctgcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCa                                              <  1:1158424/61‑1 (MQ=255)                     tCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCctc                                    >  1:502709/1‑61 (MQ=255)                     tCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCctc                                    >  1:2828567/1‑61 (MQ=255)                         ggACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTg                                  >  1:67766/1‑59 (MQ=255)                         ggACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGca                                >  1:40750/1‑61 (MQ=255)                           aCGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCAc                                                    <  1:1950646/39‑1 (MQ=255)                              aTTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:545823/62‑1 (MQ=255)                              aTTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:3834263/62‑1 (MQ=255)                              aTTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:914739/62‑1 (MQ=255)                              aTTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:2770716/62‑1 (MQ=255)                              aTTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:1364007/62‑1 (MQ=255)                               ttAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:2220265/61‑1 (MQ=255)                                    cGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACg                          <  1:3462318/56‑1 (MQ=255)                                       tAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCtttt                 >  1:306127/1‑62 (MQ=255)                                           ccGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTctg              <  1:4500089/61‑3 (MQ=255)                                           ccGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCgg              <  1:3068519/61‑1 (MQ=255)                                           ccGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCgg              <  1:4553698/61‑1 (MQ=255)                                           ccGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCgg              <  1:1911204/61‑1 (MQ=255)                                           ccGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTCCACAAACGCCACCTTTTCgg              <  1:3135798/61‑1 (MQ=39)                                             ggATCAGGCGGTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTgg           <  1:3051730/62‑1 (MQ=255)                                              gATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGc          <  1:3747588/62‑1 (MQ=255)                                              gATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGc          <  1:3559733/62‑1 (MQ=255)                                              gATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGc          <  1:2912867/62‑1 (MQ=255)                                                      gTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTa  >  1:4143562/1‑62 (MQ=255)                                                          |                                                          TTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTA  >  W3110S.gb/3213511‑3213625

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑