Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	40,228	A→G	S53S (AGT→AGC)	caiA ←	crotonobetaine reductase subunit II, FAD‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	40,228	0	A	G	100.0%	183.8 / NA	51	S53S (AGT→AGC)	caiA	crotonobetaine reductase subunit II, FAD‑binding
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/23);  total (28/23)

GTGTTGAACCCGCCCGGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGACTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGACGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTG  >  NC_000913/40100‑40362                                                                                                                                 |                                                                                                                                       gtgtTGAACCCGCCCGGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATAc                                                                                                                              <  2:872716/139‑1 (MQ=255)       aaCCCGCCCGGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCatat                                                                                                                        >  2:828907/1‑139 (MQ=255)              ccgGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGcc                                                                                                                   <  1:12422/137‑1 (MQ=255)              ccgGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGcc                                                                                                                   >  2:12422/1‑137 (MQ=255)              ccgGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAg                                                                                                                 >  2:97675/1‑139 (MQ=255)                             gCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACg                                                                                                  >  1:1039491/1‑139 (MQ=255)                                   aGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCgg                                                                                            >  1:165096/1‑139 (MQ=255)                                   aGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCgg                                                                                            >  2:405588/1‑139 (MQ=255)                                            cccccAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGa                                                                                                                                 <  2:25584/93‑1 (MQ=255)                                            cccccAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGa                                                                                                                                 >  1:25584/1‑93 (MQ=255)                                                        ccAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCa                                                                       <  1:97675/139‑1 (MQ=255)                                                                 tccaCACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCaaa                                                              >  1:223520/1‑139 (MQ=255)                                                                 tccaCACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCaaa                                                              >  2:665686/1‑139 (MQ=255)                                                                    acacGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATa                                                           <  1:828907/139‑1 (MQ=255)                                                                       cggcggCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATAc                                                                                                                              <  2:792862/69‑1 (MQ=255)                                                                       cggcggCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATAc                                                                                                                              >  1:792862/1‑69 (MQ=255)                                                                           ggcgAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTcc                                                    >  1:78137/1‑139 (MQ=255)                                                                             cgAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACaaa                                                                                                     >  2:176612/1‑88 (MQ=255)                                                                             cgAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACaaa                                                                                                     <  1:176612/88‑1 (MQ=255)                                                                                      cAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCt                                         <  2:223520/139‑1 (MQ=255)                                                                                           cccGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCa                                    <  2:165096/139‑1 (MQ=255)                                                                                             cgcgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTc                                                                    <  1:366522/105‑1 (MQ=255)                                                                                             cgcgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTc                                                                    >  2:366522/1‑105 (MQ=255)                                                                                             cgcgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCaaa                                                              >  2:414797/1‑111 (MQ=255)                                                                                             cgcgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCaaa                                                              <  1:414797/111‑1 (MQ=255)                                                                                               cgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAg                                >  2:603043/1‑139 (MQ=255)                                                                                               cgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAg                                >  1:234398/1‑139 (MQ=255)                                                                                                gTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGt                               >  2:86328/1‑139 (MQ=255)                                                                                                           cGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGatg                                                                                     <  2:222891/74‑3 (MQ=255)                                                                                                           cGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGatg                                                                                     >  1:222891/1‑72 (MQ=255)                                                                                                           cGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATAcc                    >  2:559104/1‑139 (MQ=255)                                                                                                           cGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATAcc                    >  2:157848/1‑139 (MQ=255)                                                                                                            gTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACaaa                                                                                                     >  2:771927/1‑57 (MQ=255)                                                                                                            gTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACaaa                                                                                                     <  1:771927/57‑1 (MQ=255)                                                                                                                  ttCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGt                                                                                          <  2:197930/62‑1 (MQ=255)                                                                                                                  ttCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGt                                                                                          >  1:197930/1‑62 (MQ=255)                                                                                                                   tCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACaa            <  2:234398/139‑1 (MQ=255)                                                                                                                    cAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGa                                                                                       <  2:1091177/63‑1 (MQ=255)                                                                                                                    cAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGa                                                                                       >  1:1091177/1‑63 (MQ=255)                                                                                                                     aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCa                                                                       <  2:480356/78‑1 (MQ=255)                                                                                                                     aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCa                                                                       >  1:480356/1‑78 (MQ=255)                                                                                                                     aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAAc          <  1:86328/139‑1 (MQ=255)                                                                                                                     aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAAc          <  1:405588/139‑1 (MQ=255)                                                                                                                            agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGt                                                                                          >  1:797987/1‑52 (MQ=255)                                                                                                                            agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGt                                                                                          <  2:797987/52‑1 (MQ=255)                                                                                                                            agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGt                                                                                 >  1:897618/1‑61 (MQ=255)                                                                                                                            agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGt                                                                                 <  2:897618/61‑1 (MQ=255)                                                                                                                            agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGACGCTGTCACGGTCGCa                                                                       <  2:756627/71‑1 (MQ=255)                                                                                                                            agcagGCTGTCGATACCCACATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCa                                                                       >  1:756627/1‑71 (MQ=255)                                                                                                                             gcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTg  <  2:1039491/139‑1 (MQ=255)                                                                                                                              cagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTc                                                                    >  1:305374/1‑72 (MQ=255)                                                                                                                                 |                                                                                                                                       GTGTTGAACCCGCCCGGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGACTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGACGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTG  >  NC_000913/40100‑40362

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑