Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,977,972	T→C	T76A (ACT→GCT)	flhD ←	DNA‑binding transcriptional dual regulator FlhD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,977,972	0	T	C	100.0%	215.2 / NA	58	T76A (ACT→GCT)	flhD	DNA‑binding transcriptional dual regulator FlhD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (35/23);  total (35/23)

ATCAGGCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTATGCCGAGA  >  NC_000913/1977846‑1978093                                                                                                                               |                                                                                                                          aTCAGGCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCtggtgg                                                                                                              >  1:53842/1‑140 (MQ=255) aTCAGGCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCtggtgg                                                                                                              >  1:279284/1‑140 (MQ=255)     ggCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGt                                                                                                          <  2:53842/140‑1 (MQ=255)     ggCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGt                                                                                                          >  1:1167144/1‑140 (MQ=255)      gCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTc                                                                                                         >  2:1164853/1‑140 (MQ=255)      gCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTc                                                                                                         >  2:866139/1‑140 (MQ=255)         cTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGATGGCTGTCaaa                                                                                                      <  2:484780/140‑1 (MQ=255)          ttttCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCaaaa                                                                                                     >  1:1176437/1‑140 (MQ=255)              cTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGa                                                                                                 <  1:894258/140‑1 (MQ=255)                  cgcAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTg                                                                                             >  1:377676/1‑140 (MQ=255)                     aGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTCAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACa                                                                                          <  2:1153438/140‑1 (MQ=255)                       cgcTTCTTCAGGCTGATTAGCATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACaaa                                                                                        >  1:1192116/1‑140 (MQ=255)                       cgcTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACaaa                                                                                        >  2:880087/1‑140 (MQ=255)                           tcttcAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAg                                                                                    <  1:1180808/140‑1 (MQ=255)                           tcttcAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAg                                                                                    <  2:1176437/140‑1 (MQ=255)                            cttcAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGt                                                                                   >  2:32619/1‑140 (MQ=255)                                 ggCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGAtt                                                                              >  1:708437/1‑140 (MQ=255)                                  gCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTg                                                                             >  1:1008153/1‑140 (MQ=255)                                      aTTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGttt                                                                         >  1:521946/1‑140 (MQ=255)                                      aTTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGttt                                                                         >  1:646847/1‑140 (MQ=255)                                      aTTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGttt                                                                         >  2:234061/1‑140 (MQ=255)                                      aTTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGttt                                                                         >  1:965881/1‑140 (MQ=255)                                          aCATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGc                                                                     <  1:558506/140‑1 (MQ=255)                                          aCATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGc                                                                     <  2:646847/140‑1 (MQ=255)                                          aCATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGc                                                                     <  2:1008153/140‑1 (MQ=255)                                          aCATCATTCAGCAAGCGTGTTAAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGc                                                                     <  2:1123842/140‑1 (MQ=255)                                                ttCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCtt                                                               >  1:232495/1‑140 (MQ=255)                                                ttCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCtt                                                               >  1:801712/1‑140 (MQ=255)                                                ttCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTACTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTTCCAGCtt                                                               >  2:1041925/1‑140 (MQ=255)                                                ttCAGCAAGCGTGTTGAGAGCATGATACCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCtt                                                               >  2:514743/1‑140 (MQ=255)                                                        gCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCAttt                                                       >  1:105224/1‑140 (MQ=255)                                                        gCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCAttt                                                       >  2:1132472/1‑140 (MQ=255)                                                         cGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTg                                                      >  1:852191/1‑140 (MQ=255)                                                         cGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTACCAGCTTAAcc                                                           <  2:835970/135‑1 (MQ=255)                                                         cGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTACCAGCTTAAcc                                                           >  1:835970/1‑135 (MQ=255)                                                           tgtTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCg                                                    >  1:100399/1‑140 (MQ=255)                                                            gtTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCgg                                                   <  1:1132472/140‑1 (MQ=255)                                                             ttGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGa                                                  <  2:141856/140‑1 (MQ=255)                                                                  agCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTTATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGt                                             >  2:1167351/1‑140 (MQ=255)                                                                    cATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCa                                           >  1:5717/1‑140 (MQ=255)                                                                    cATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCa                                           <  2:521946/140‑1 (MQ=255)                                                                     atgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAg                                          <  1:75385/140‑1 (MQ=255)                                                                     atgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAg                                          <  2:1063109/140‑1 (MQ=255)                                                                     atgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAg                                          >  2:1129549/1‑140 (MQ=255)                                                                     atgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAg                                          >  1:1063109/1‑140 (MQ=255)                                                                     atgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAg                                          <  2:279284/140‑1 (MQ=255)                                                                     atgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAg                                          <  1:880087/140‑1 (MQ=255)                                                                      tgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGt                                         >  1:361628/1‑140 (MQ=255)                                                                      tgatgCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGt                                         <  2:708437/140‑1 (MQ=255)                                                                          gCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAaga                                               <  2:901811/130‑1 (MQ=255)                                                                          gCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAaga                                               >  1:901811/1‑130 (MQ=255)                                                                                        gCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGcc                       <  1:266954/140‑1 (MQ=255)                                                                                        gCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGCGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGcc                       >  2:1036491/1‑140 (MQ=255)                                                                                             agaTCGTCAACGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATttc                  >  1:362489/1‑140 (MQ=255)                                                                                                      aCGCGGGAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTAt         >  2:1053125/1‑140 (MQ=255)                                                                                                           ggAATCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTATGCCga    >  1:104489/1‑140 (MQ=255)                                                                                                             aaTCTTGCGTCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTATGCCgaga  <  2:5717/140‑1 (MQ=255)                                                                                                                      tCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTATGCCgag   >  2:314944/1‑130 (MQ=255)                                                                                                                      tCAACTGAGCAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTATGCCgag   <  1:314944/130‑1 (MQ=255)                                                                                                                               |                                                                                                                          ATCAGGCCCTTTTCTTGCGCAGCGCTTCTTCAGGCTGATTAACATCATTCAGCAAGCGTGTTGAGAGCATGATGCCGGTATGAATTTGCTGGAGATCGTCAACGCGGGAATCTTGCGTCAACTGAGTAATCGTCTGGTGGCTGTCAAAACGGAAGTGACAAACCAGTTGATTGGTTTCTGCCAGCTTAACCATTTGCGGAAGAGTCAGTGCCGCTAACGTTGTCGCCATTTCTTCATTTATGCCGAGA  >  NC_000913/1977846‑1978093

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑