Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,351,784	T→C	intergenic (‑122/‑59)	dcuS ← / → yjdI	sensory histidine kinase DcuS/PF06902 family protein YjdI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,351,784	0	T	C	100.0%	178.7 / NA	50	intergenic (‑122/‑59)	dcuS/yjdI	sensory histidine kinase DcuS/PF06902 family protein YjdI
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/35);  total (15/35)

AATGAATGTCTCATCAGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGTATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTCTATTTCAACACTGCGA  >  NC_000913/4351649‑4351918                                                                                                                                        |                                                                                                                                       aatgaatgTCTCATCAGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGATATATAGGGGAACAGATTCTGGCAAGGGAAACTGCCAGTGCTGCATGa                                                                                                                                    >  2:265342/1‑140 (MQ=255)       tgTCTCATCAGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTc                                                                                                                              <  1:382439/140‑1 (MQ=255)             atcaGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGGGGAAGAATGATTGGGTATATATGGGAGGAGACTCTTGCATCGGAAACTGCCAGTGCTACCTGAAGATTTCGGGGc                                                                                                                        >  2:249393/1‑140 (MQ=255)              tcaGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCt                                                                                                                       <  1:140612/140‑1 (MQ=255)                aGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTAt                                                                                                                     <  1:683208/140‑1 (MQ=255)                aGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTAt                                                                                                                     <  1:477180/140‑1 (MQ=255)                     ccTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTta                                                                                                                <  1:540888/140‑1 (MQ=255)                         gtgtgACAAATTTCTTGCGCATGATCTCTGCTGCGTCGGGTAATTCAATGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  2:351845/140‑1 (MQ=255)                         gtgtgACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  1:646920/140‑1 (MQ=255)                         gtgtgACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  2:475542/140‑1 (MQ=255)                         gtgtgACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  1:620773/140‑1 (MQ=255)                         gtgtgACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  2:2224/140‑1 (MQ=255)                         gtgtgACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  2:34641/140‑1 (MQ=255)                         gtgtgACAAATTTCTTAAGCATAATATCTCATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGc                                                                                                            <  1:249207/140‑1 (MQ=255)                            tgACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGAt                                                                                                         <  1:132380/140‑1 (MQ=255)                              aCAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATaa                                                                                                       <  1:441835/140‑1 (MQ=255)                              aCAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATaa                                                                                                       <  2:457391/140‑1 (MQ=255)                               cAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCAAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAAt                                                                                                      >  2:639438/1‑140 (MQ=255)                                    ttCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATAc                                                                                                 <  1:68430/140‑1 (MQ=255)                                        tAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACtgat                                                                                             <  2:174990/140‑1 (MQ=255)                                                 tctcTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAggg                                                                                    <  2:374366/140‑1 (MQ=255)                                                 tctcTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAggg                                                                                    <  1:676856/140‑1 (MQ=255)                                                 tctcTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAggg                                                                                    <  2:106732/140‑1 (MQ=255)                                                  ctctGATGAGGCGGGTAATTCACAGGGAGTAAGAATGCTTGGCTATATAGGGGAAGAGACTCTGACAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGa                                                                                   <  1:296469/140‑1 (MQ=255)                                                  ctctGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGa                                                                                   <  1:488748/140‑1 (MQ=255)                                                  ctctGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGa                                                                                   <  2:20678/140‑1 (MQ=255)                                                  ctctGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGa                                                                                   <  2:171161/140‑1 (MQ=255)                                                       atgaGGCGGGTAATTCAAAGGGGGGAAGAATGATTGGCTATATAGGGGGAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAgggc                                                                              >  2:361578/1‑138 (MQ=255)                                                            gCGGGTAATTCCAAGGGGGGAAGAATGATTGGCTATATAGGGGAAGAGACTCTTGCAACGGGAACTGCCAGTGCTGCATGAAAAATCCGGGGCCATGCTTATAACGATAATGATACTGATGAGGGAGGGGAGGGCATGGa                                                                         >  2:102062/1‑140 (MQ=255)                                                            gCGGGGAAGTCAAAAGGAGAAAGAATGATTGGCTATATAGGGGAAGAAACTCTGACAAAGGGAAACGCCCGAGCCGCCCTAATATTCCGGGTCGATGCTTATAGTGCGGATCATACTGATGAAAGAGGGAAAGGCATGGa                                                                         >  2:296469/1‑140 (MQ=255)                                                                          gggAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTgg                                                           >  2:567968/1‑140 (MQ=255)                                                                           ggAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCAAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGa                                                          <  1:639438/140‑1 (MQ=255)                                                                             aGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTTATGAGAGCGGGAAGGTGATGGATCAGGCGCTACTGGACg                                                        >  2:245604/1‑140 (MQ=255)                                                                             aGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGAAGAGAGAGAGAACGTCATGGATCAGGCGCTACTGGACg                                                        >  1:315690/1‑140 (MQ=255)                                                                              gTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACgg                                                       >  1:446404/1‑140 (MQ=255)                                                                                     tGATTGGCTATATAGGGTAAGAGACTCTGGCTACGGAAATTGCCAGTGTTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTAt                                                <  2:258132/140‑1 (MQ=255)                                                                                     tGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTAc                                                              <  2:663999/126‑1 (MQ=255)                                                                                     tGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTAc                                                              >  1:663999/1‑126 (MQ=255)                                                                                     tGATTGGCTATATAGGGGAAGAGACCCTGGCAACGGAGACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTAt                                                <  1:265342/140‑1 (MQ=255)                                                                                                      gAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGa                               >  2:650648/1‑140 (MQ=255)                                                                                                      gAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGa                               >  2:491509/1‑140 (MQ=255)                                                                                                         gagaCTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGGTACTGGACGGGAGTAATCGCTGTTATACCGGCGaaaa                            >  1:249187/1‑140 (MQ=255)                                                                                                         gagaCTCTGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGaaaa                            >  2:14825/1‑140 (MQ=255)                                                                                                             ctctGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATGATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGAC‑GGGGTTATCGCTGTTATACCGGCGAAAAGATCg                       <  1:102062/140‑1 (MQ=255)                                                                                                              tctGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCg                       >  1:38450/1‑140 (MQ=255)                                                                                                              tctGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCg                       >  1:165793/1‑140 (MQ=255)                                                                                                              tctGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCg                       >  1:164940/1‑140 (MQ=255)                                                                                                              tctGGCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCg                       >  2:565876/1‑140 (MQ=255)                                                                                                                 ggCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATg                    <  1:565876/140‑1 (MQ=255)                                                                                                                 ggCAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATg                    <  1:14825/140‑1 (MQ=255)                                                                                                                   cAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTc                  <  1:491509/140‑1 (MQ=255)                                                                                                                   cAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTc                  <  2:613952/140‑1 (MQ=255)                                                                                                                   cAACGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTc                  <  2:164940/140‑1 (MQ=255)                                                                                                                    aaCGGAAACTGCCAGTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTCt                 >  2:177817/1‑140 (MQ=255)                                                                                                                                  gTGCTGCATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTCTATTTCAACACTGCg   <  1:650648/140‑1 (MQ=255)                                                                                                                                   tgctgcATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTCTATTTCAACACTGCGa  <  2:463382/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                       AATGAATGTCTCATCAGCTTCCTTGTGTGACAAATTTCTTAAGCATTATCTCTGATGAGGCGGGTAATTCAAAGGGAGTAAGAATGATTGGCTATATAGGGGAAGAGACTCTGGCAACGGAAACTGCCAGTGCTGTATGAAGATTCCGGGGCTATGCTTATAGCGATAATCATACTGATGAGAGAGGGAAGGTCATGGATCAGGCGCTACTGGACGGGGGTTATCGCTGTTATACCGGCGAAAAGATCGATGTCTATTTCAACACTGCGA  >  NC_000913/4351649‑4351918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑