Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,559,491	G→A	W408* (TGG→TGA)	rtcR →	DNA‑binding transcriptional activator RtcR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,559,491	0	G	A	100.0%	160.1 / NA	44	W408* (TGG→TGA)	rtcR	DNA‑binding transcriptional activator RtcR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/27);  total (17/27)

ACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGG  >  NC_000913/3559414‑3559567                                                                              |                                                                             actGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGacgc                                                                           <  2:676436/81‑1 (MQ=255) actGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGacgc                                                                           <  2:676438/81‑1 (MQ=255)     gCGACAGCGTGCGTTTTACCACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCTACCTCTCCCCAGGCAACATGACGCGGTa                                                                       <  1:676439/81‑1 (MQ=255)        aCAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACt                                                                    >  2:676506/1‑81 (MQ=255)          aGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACttt                                                                  >  2:676521/1‑81 (MQ=255)           gcgtgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTc                                                                 <  1:676440/81‑1 (MQ=255)           gcgtgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTc                                                                 <  2:676441/81‑1 (MQ=255)            cgtgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTcg                                                                <  1:676442/81‑1 (MQ=255)              tgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTcgcg                                                              <  2:676443/81‑1 (MQ=255)                 gtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAAc                                                           <  1:676444/81‑1 (MQ=255)                    ttAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACtt                                                         <  1:676445/80‑1 (MQ=255)                     tAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACttt                                                        <  2:676446/80‑1 (MQ=255)                     tAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACttt                                                        <  2:676447/80‑1 (MQ=255)                      aaCACCGAAGCGCTGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCt                                                      >  1:676519/1‑81 (MQ=255)                      aaCACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTc                                                       <  2:676448/80‑1 (MQ=255)                       acacCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCt                                                      <  2:676449/80‑1 (MQ=255)                         acCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGcc                                                   <  2:676451/81‑1 (MQ=255)                         acCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGcc                                                   <  1:676450/81‑1 (MQ=255)                           cGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAg                                                 <  1:676452/81‑1 (MQ=255)                            gAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGc                                                >  1:676523/1‑81 (MQ=255)                             aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCg                                               >  1:676503/1‑81 (MQ=255)                             aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCg                                               <  1:676453/81‑1 (MQ=255)                                 gcggcgcgCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCAc                                           >  2:676528/1‑81 (MQ=255)                                   ggcgcgCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCAcgc                                         >  1:676516/1‑81 (MQ=255)                                     cgcgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCgg                                       <  1:676454/81‑1 (MQ=255)                                     cgcgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCgg                                       <  1:676455/81‑1 (MQ=255)                                       cgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGAt                                     <  2:676456/81‑1 (MQ=255)                                        gcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATg                                    >  1:676517/1‑81 (MQ=255)                                            ggTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCa                                >  2:676525/1‑81 (MQ=255)                                             gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGcc                                 <  2:676458/79‑1 (MQ=255)                                             gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGcc                                 <  1:676459/79‑1 (MQ=255)                                             gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCa                                <  1:676457/80‑1 (MQ=255)                                             gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCAc                               <  2:676460/81‑1 (MQ=255)                                                 gCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCttt                           <  1:676462/81‑1 (MQ=255)                                                 gCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCttt                           <  2:676461/81‑1 (MQ=255)                                                    tttGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGc                         >  1:676508/1‑80 (MQ=255)                                                    tttGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGc                         >  2:676511/1‑80 (MQ=255)                                                         gACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAg                   >  1:676518/1‑81 (MQ=255)                                                          aCCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGc                  <  1:676463/81‑1 (MQ=255)                                                             tctcCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGa               >  1:676513/1‑81 (MQ=255)                                                              ctcCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGAc              >  1:676504/1‑81 (MQ=255)                                                                ccccAGGCAATATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACg             >  2:676520/1‑80 (MQ=255)                                                                ccccAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACg             >  1:676515/1‑80 (MQ=255)                                                                  ccAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCAt          >  1:676507/1‑81 (MQ=255)                                                                   cAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATc         <  1:676464/81‑1 (MQ=255)                                                                          cATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTgg  <  1:676465/81‑1 (MQ=255)                                                                              |                                                                             ACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGG  >  NC_000913/3559414‑3559567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑