Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,321,836	C→T	C196Y (TGC→TAC)	phnF ←	putative transcriptional regulator PhnF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,321,836	0	C	T	100.0%	185.0 / NA	54	C196Y (TGC→TAC)	phnF	putative transcriptional regulator PhnF
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/22);  total (32/22)

GTGCTCCATAGTGAATTCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGC  >  NC_000913/4321700‑4321972                                                                                                                                         |                                                                                                                                         gTGCTCCATAGTGAATTCAATCATGTCGGCGCGCGTCAGGCTGACTGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTAct                                                                                                                                       >  2:900372/1‑140 (MQ=255)    cTCCATAGTGAATTCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCtt                                                                                                                                    >  2:1062493/1‑140 (MQ=255)        aTAGTGAATTTAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGc                                                                                                                                <  1:303651/140‑1 (MQ=255)         tAGTGAATTCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGcc                                                                                                                               >  2:324265/1‑140 (MQ=255)              aaTTCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGgc                                                                                                                          >  2:852305/1‑140 (MQ=255)              aaTTCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGgc                                                                                                                          >  2:1148220/1‑140 (MQ=255)                ttCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGgcgc                                                                                                                        >  1:19567/1‑140 (MQ=255)                 tCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGcgcg                                                                                                                       >  1:902794/1‑140 (MQ=255)                   aaTCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCgcggc                                                                                                                     <  2:902794/140‑1 (MQ=255)                   aaTCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCgcggc                                                                                                                     <  1:920254/140‑1 (MQ=255)                    aTCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCgcggcg                                                                                                                    >  1:416021/1‑140 (MQ=255)                      cATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCggcggg                                                                                                                  >  2:168622/1‑140 (MQ=255)                         gTCGGCGCGCGTCAGGCTGACTGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGgcgc                                                                                                               <  1:900372/140‑1 (MQ=255)                                   gTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGt                                                                                                     <  1:852305/140‑1 (MQ=255)                                                         ccgGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGgcgcagcg                                                                                    >  2:861357/1‑135 (MQ=255)                                                         ccgGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGgcgcagcg                                                                                    <  1:861357/135‑1 (MQ=255)                                                          cgGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTc                                                                              >  1:378189/1‑140 (MQ=255)                                                            ggCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCg                                                                            >  2:596977/1‑140 (MQ=255)                                                            ggCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCg                                                                            >  1:793924/1‑140 (MQ=255)                                                               tgctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTgcggcg                                                                                         <  2:525511/124‑1 (MQ=255)                                                               tgctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTgcggcg                                                                                         <  2:276060/124‑1 (MQ=255)                                                               tgctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTgcggcg                                                                                         >  1:276060/1‑124 (MQ=255)                                                               tgctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTgcggcg                                                                                         >  1:525511/1‑124 (MQ=255)                                                                 ctTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGGCTGGCTGCGGCGCCGCGCAATTCCGGGTTg                                                                       >  2:323646/1‑140 (MQ=255)                                                                                     aaGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCa                                                   >  1:55117/1‑140 (MQ=255)                                                                                         gTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGACGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCgg                                               >  2:871869/1‑139 (MQ=255)                                                                                          tGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGa                                                             >  1:865919/1‑125 (MQ=255)                                                                                          tGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGa                                                             <  2:865919/125‑1 (MQ=255)                                                                                           gcgcACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGc                                             <  2:55117/140‑1 (MQ=255)                                                                                            cgcacgcaCAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGcc                                            >  1:631914/1‑140 (MQ=255)                                                                                            cgcacgcaCAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGcc                                            >  2:607608/1‑140 (MQ=255)                                                                                            cgcacgcaCAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGcc                                            >  1:985869/1‑140 (MQ=255)                                                                                             gcacgcacAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCg                                           <  1:596977/140‑1 (MQ=255)                                                                                                 gcacAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTCGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGt                                       <  2:793924/140‑1 (MQ=255)                                                                                                    cagcagCGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGa                                    >  1:1049708/1‑140 (MQ=255)                                                                                                      gcagcGGCGACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAg                                  <  2:631914/140‑1 (MQ=255)                                                                                                         gcggcgACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGt                               >  1:269688/1‑140 (MQ=255)                                                                                                           ggcgACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGaa                                   >  2:995548/1‑134 (MQ=255)                                                                                                           ggcgACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGaa                                   <  1:995548/134‑1 (MQ=255)                                                                                                           ggcgACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTg                             >  1:576957/1‑140 (MQ=255)                                                                                                              gACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTg                             >  2:1041741/1‑137 (MQ=255)                                                                                                              gACATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTg                             <  1:1041741/137‑1 (MQ=255)                                                                                                               aCATATTCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGc                         >  1:3084/1‑140 (MQ=255)                                                                                                                     tCGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGc                   <  2:576957/140‑1 (MQ=255)                                                                                                                      cGGGATTTCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGcc                  <  1:297055/140‑1 (MQ=255)                                                                                                                            ttCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCa                           >  2:820396/1‑125 (MQ=255)                                                                                                                            ttCAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCa                           <  1:820396/125‑1 (MQ=255)                                                                                                                              cAAGACGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTg          <  2:1049708/140‑1 (MQ=255)                                                                                                                                  aCGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGt      <  2:269688/140‑1 (MQ=255)                                                                                                                                  aCGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGt      <  1:607608/140‑1 (MQ=255)                                                                                                                                   cGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGGCGTGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATTCCGCAGCGAGCCGCCGTCGAAGCGTTGCAGCGTCGGCCCGAGGGAGAGGTc     >  2:914500/1‑140 (MQ=255)                                                                                                                                   cGCTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTc     >  1:519984/1‑140 (MQ=255)                                                                                                                                     cTGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCcg   <  2:416021/140‑1 (MQ=255)                                                                                                                                      tGGTACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCACCGCAATTTCCGGTTGCTCGCGCAGAAAAACGTGCAGCGGGCCCCTGTCGAAGCGTTGCAGGGTCCGGCAGAGGGGGAGGGCcgc  >  2:584895/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                         GTGCTCCATAGTGAATTCAATCATGTCGGCGCGCGTCAGGCTGACGGAGTACTCCGCCGGGCTGCTTTCACCGTCACGGTGGTTAAGGGTGCGCACGCACAGCAGCGGCGACATATTCGGGATTTCAAGACGCTGGCACTCTTTGGCCTGGGCGCGGCGGGCGCTGATCCGCGTCTGGCTGCGGCGCAGCGCAATTCCGGTTTGCTCGCGCAGAAAATCGTGCAGCGAGCCGCTGTCGAAGCGTTGCAGCGTCGGCCAGAGGGTGAGGTCCGC  >  NC_000913/4321700‑4321972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑