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%	170.6 / NA	49	S53S (AGT→AGC)	caiA	crotonobetaine reductase subunit II, FAD‑binding
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (24/25);  total (24/25)

CAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGACTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGACGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTGC  >  NC_000913/40117‑40363                                                                                                                |                                                                                                                                        cAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCt                                                                                                              <  1:974138/139‑1 (MQ=255) cAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCt                                                                                                              <  2:622793/139‑1 (MQ=255)       gTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACa                                                                                                        <  2:1756927/139‑1 (MQ=255)             cacaTAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGt                                                                                                  >  1:1933955/1‑139 (MQ=255)              acaTAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGtt                                                                                                 <  1:1815631/139‑1 (MQ=255)              acaTAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGtt                                                                                                 <  1:530197/139‑1 (MQ=255)                       ggTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCt                                                                                                              <  1:1749224/117‑1 (MQ=255)                       ggTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCt                                                                                                              >  2:1749224/1‑117 (MQ=255)                       ggTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCggg                                                                                            <  2:616579/135‑1 (MQ=255)                       ggTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCggg                                                                                            >  1:616579/1‑135 (MQ=255)                       ggTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGa                                                                                        >  1:1311344/1‑139 (MQ=255)                                                tccaCACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTc                                                                                                >  1:1253445/1‑106 (MQ=255)                                                tccaCACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTc                                                                                                <  2:1253445/106‑1 (MQ=255)                                                     acGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTc                                                                                                <  2:1891454/101‑1 (MQ=255)                                                     acGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTc                                                                                                >  1:1891454/1‑101 (MQ=255)                                                     acGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAgg                                                          >  2:983910/1‑139 (MQ=255)                                                     acGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAgg                                                          <  1:983910/139‑1 (MQ=255)                                                        gcggcgAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCt                                                       >  1:523665/1‑139 (MQ=255)                                                          ggcgAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTcc                                                     <  2:1311344/139‑1 (MQ=255)                                                           gcgAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTccc                                                    >  1:1913869/1‑139 (MQ=255)                                                              agagTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCa                                                                        <  1:912377/116‑1 (MQ=255)                                                              agagTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCa                                                                        >  2:912377/1‑116 (MQ=255)                                                                   aaCAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGt                                                                                           <  2:1983598/92‑1 (MQ=255)                                                                   aaCAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGt                                                                                           >  1:1983598/1‑92 (MQ=255)                                                                     cAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCt                                          <  2:1933955/139‑1 (MQ=255)                                                                              cgTCCAGACCACCGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAg                                 >  2:1252438/1‑139 (MQ=255)                                                                                       caccGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCt                                                                                                              <  1:790245/53‑1 (MQ=255)                                                                                       caccGTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCt                                                                                                              >  2:790245/1‑53 (MQ=255)                                                                                           gTGCTCTTCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCg                    >  2:761699/1‑139 (MQ=255)                                                                                                 ttCAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACa              <  1:761699/139‑1 (MQ=255)                                                                                                   cAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTcc                                                     >  2:1553505/1‑98 (MQ=255)                                                                                                   cAGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTcc                                                     <  1:1553505/98‑1 (MQ=255)                                                                                                    aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACACAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAAc           <  1:1252438/139‑1 (MQ=255)                                                                                                    aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAAc           <  2:523665/139‑1 (MQ=255)                                                                                                    aGGGATCAGCAGGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAAc           <  2:188554/139‑1 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACaa                                                                                                       >  1:820469/1‑40 (MQ=38)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACaa                                                                                                       <  2:820469/40‑1 (MQ=38)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGtt                                                                                                 <  2:991418/46‑1 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGtt                                                                                                 >  1:991418/1‑46 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCgg                                                                   <  2:314247/76‑1 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCgg                                                                   <  2:1134537/76‑1 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCgg                                                                   >  1:314247/1‑76 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCgg                                                                   >  1:1134537/1‑76 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGt        >  2:1855083/1‑135 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGt        <  1:1855083/135‑1 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCt    >  2:1173300/1‑139 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCt    >  2:1078577/1‑139 (MQ=255)                                                                                                           agcagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCt    >  1:584178/1‑139 (MQ=255)                                                                                                             cagGCTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGATGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTGc  >  1:661890/1‑139 (MQ=255)                                                                                                                |                                                                                                                                        CAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGCGAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGACTGTCGATACCCATATCCGCCAGTGCTTTGACAAAACGTTCCGGGTAGACGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGTTTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTGC  >  NC_000913/40117‑40363

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑