Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,244,167	C→T	A121T (GCC→ACC)	ycgR ←	flagellar velocity braking protein, c‑di‑GMP‑regulated

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,244,167	0	C	T	100.0%	194.8 / NA	60	A121T (GCC→ACC)	ycgR	flagellar velocity braking protein, c‑di‑GMP‑regulated
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (26/34);  total (26/34)

CTTGTAATTCGGCAGGCTTTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGCGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTATTCACTCTGCTGTAGTTGTT  >  NC_000913/1244035‑1244268                                                                                                                                     |                                                                                                      cttGTAATTCGGCAGGCTTTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGga                                                                                                    >  1:864136/1‑136 (MQ=255) cttGTAATTCGGCAGGCTCTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGga                                                                                                    <  2:864136/136‑1 (MQ=255)             cAGGCTTTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCg                                                                                     <  2:679033/139‑1 (MQ=255)              aGGCTTTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCgg                                                                                    <  1:626952/139‑1 (MQ=255)                gCTTTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGcg                                                                                  >  1:192740/1‑139 (MQ=255)                   ttGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGcgtcg                                                                               <  2:692551/139‑1 (MQ=255)                   ttGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGcgtcg                                                                               <  1:146336/139‑1 (MQ=255)                      cTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTg                                                                            <  2:434189/139‑1 (MQ=255)                               gTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCa                                                                   <  2:648274/139‑1 (MQ=255)                                     cgcCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACa                                                                        <  1:517838/128‑1 (MQ=255)                                     cgcCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACa                                                                        >  2:517838/1‑128 (MQ=255)                                     cgcCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGt                                                             >  2:263263/1‑139 (MQ=255)                                                ccTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcggta                                                  >  2:1353828/1‑139 (MQ=255)                                                 cTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcggtac                                                 <  1:263263/139‑1 (MQ=255)                                                          aaTCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGgaga                                                                                                  >  1:1300494/1‑81 (MQ=255)                                                          aaTCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGgaga                                                                                                  <  2:1300494/81‑1 (MQ=255)                                                           aTCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTg                                                            <  2:153734/118‑1 (MQ=255)                                                           aTCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTg                                                            >  1:153734/1‑118 (MQ=255)                                                               tACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCg                                   <  1:975873/139‑1 (MQ=255)                                                                   ggCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCAt                                                                  >  1:1021067/1‑104 (MQ=255)                                                                   ggCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCAt                                                                  <  2:1021067/104‑1 (MQ=255)                                                                    gCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGc                              <  2:192740/139‑1 (MQ=255)                                                                     cGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcggta                                                  >  1:1474189/1‑118 (MQ=255)                                                                     cGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcggta                                                  <  2:1474189/118‑1 (MQ=255)                                                                      ggAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTg                            <  2:653672/139‑1 (MQ=255)                                                                      ggAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTg                            <  2:400297/139‑1 (MQ=255)                                                                      ggAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTg                            <  1:1353828/139‑1 (MQ=255)                                                                              aacgtaCTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTa                                                                          >  2:265494/1‑85 (MQ=255)                                                                              aacgtaCTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTa                                                                          <  1:265494/85‑1 (MQ=255)                                                                              aacgtaCTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTAtt                    >  2:1307337/1‑139 (MQ=255)                                                                                  taCTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcgg                                                    >  1:753160/1‑103 (MQ=255)                                                                                  taCTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcgg                                                    <  2:753160/103‑1 (MQ=255)                                                                                     tGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCg                                                                                     >  1:1323290/1‑67 (MQ=255)                                                                                     tGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCg                                                                                     <  2:1323290/67‑1 (MQ=255)                                                                                     tGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGcgtcg                                                                               <  1:709017/73‑1 (MQ=255)                                                                                     tGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGcgtcg                                                                               >  2:709017/1‑73 (MQ=255)                                                                                      gTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACa                                                                        <  1:1060178/79‑1 (MQ=255)                                                                                      gTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACa                                                                        >  2:1060178/1‑79 (MQ=255)                                                                                      gTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGtaataa                                         >  1:214198/1‑110 (MQ=255)                                                                                      gTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGtaataa                                         <  2:214198/110‑1 (MQ=255)                                                                                          tCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTATTCACTCTGCTGTa        >  1:1346380/1‑139 (MQ=255)                                                                                            cGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcggta                                                  <  2:433387/95‑1 (MQ=255)                                                                                            cGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGcggta                                                  >  1:433387/1‑95 (MQ=255)                                                                                            cGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGa                                 <  1:250277/112‑1 (MQ=255)                                                                                            cGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGa                                 >  2:250277/1‑112 (MQ=255)                                                                                                aGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTATTCACTCTGCTGTAgttgtt  <  2:1346380/139‑1 (MQ=255)                                                                                                       tCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTAt                     <  2:391917/113‑1 (MQ=255)                                                                                                       tCTGGCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTAt                     >  1:391917/1‑113 (MQ=255)                                                                                                           gCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTATTCAc                 <  1:1155230/113‑1 (MQ=255)                                                                                                           gCAAAAATAAGGCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTATTCAc                 >  2:1155230/1‑113 (MQ=255)                                                                                                                     ggtggATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCa                          <  2:35870/91‑1 (MQ=255)                                                                                                                     ggtggATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCa                          >  1:35870/4‑94 (MQ=255)                                                                                                                     ggCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGa                                                         >  1:1294858/1‑63 (MQ=255)                                                                                                                     ggCGGATGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGa                                                         <  2:1294858/63‑1 (MQ=255)                                                                                                                          aTGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTAc                                                                         <  2:532572/42‑1 (MQ=255)                                                                                                                          aTGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTAc                                                                         >  1:532572/1‑42 (MQ=255)                                                                                                                           tGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGa                                 <  2:1092214/81‑1 (MQ=255)                                                                                                                           tGGAGTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGa                                 >  1:1092214/1‑81 (MQ=255)                                                                                                                               gTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGc                           >  1:338977/1‑83 (MQ=255)                                                                                                                               gTGGGGTGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGc                           <  2:338977/83‑1 (MQ=255)                                                                                                                                     |                                                                                                      CTTGTAATTCGGCAGGCTTTGCTGTTTCCAGTAATGCGCCCATGCCGCCTAACGACAAATCATACAGGCGGAAACGTAACGTACTGTTATCCGCCAGTTTGGTCTGGCAAAAATAAGGCGGATGGAGTGGGGCGGAGATGCGGAAATATCGGCGTCGTTGTACAAACCATAAGGTGGGAGGCGGTACGGTAATAAATGCCGGAAGCTGCAAGTATTCACTCTGCTGTAGTTGTT  >  NC_000913/1244035‑1244268

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: ‑