Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,023,726	A→C	intergenic (+48/‑242)	fliR → / → rcsA	flagellar biosynthesis protein FliR/DNA‑binding transcriptional activator RcsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,023,726	0	A	C	100.0%	158.7 / NA	41	intergenic (+48/‑242)	fliR/rcsA	flagellar biosynthesis protein FliR/DNA‑binding transcriptional activator RcsA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (23/18);  total (23/18)

CCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTC  >  NC_000913/2023592‑2023855                                                                                                                                       |                                                                                                                                  ccGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTAc                                                                                                                              <  2:481026/140‑1 (MQ=255)   gTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGa                                                                                                                            >  1:282237/1‑140 (MQ=255)   gTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGa                                                                                                                            >  2:314556/1‑140 (MQ=255)      aaTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACa                                                                                                                         <  1:235750/140‑1 (MQ=255)      aaTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACa                                                                                                                         <  2:169030/140‑1 (MQ=255)      aaTTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACa                                                                                                                         <  1:314556/140‑1 (MQ=255)                                    tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGa                                                                                                 >  1:107165/1‑134 (MQ=255)                                    tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGa                                                                                                 <  2:107165/134‑1 (MQ=255)                                    tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATAtt                                                                                           >  2:193155/1‑140 (MQ=255)                                             tAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAg                                                                                  <  2:282237/140‑1 (MQ=255)                                             tAATTTGCTGGCTGATATAATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAg                                                                                  <  2:109806/140‑1 (MQ=255)                                               aTTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGct                                                                                <  2:448535/140‑1 (MQ=255)                                                                 ttaGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACa                                                              >  1:311473/1‑140 (MQ=255)                                                                     tGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcactca                                                                          >  1:396335/1‑124 (MQ=255)                                                                     tGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcactca                                                                          <  2:396335/124‑1 (MQ=255)                                                                         ttGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttacttt                                                      >  2:97365/1‑140 (MQ=255)                                                                                 aaTATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAg                                              >  2:223794/1‑140 (MQ=255)                                                                                        ttCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTc                                       >  1:237055/1‑140 (MQ=255)                                                                                             tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGc                                  >  1:369158/1‑140 (MQ=255)                                                                                             tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGc                                  >  1:261035/1‑140 (MQ=255)                                                                                                cGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCaaa                               <  2:311473/140‑1 (MQ=255)                                                                                                        aTGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATacaa                       <  1:223794/140‑1 (MQ=255)                                                                                                        aTGTTATCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATacaa                       <  2:237055/140‑1 (MQ=255)                                                                                                             aTCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATacaaca                     >  1:8180/1‑137 (MQ=255)                                                                                                             aTCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATacaaca                     <  2:8180/137‑1 (MQ=255)                                                                                                             aTCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACtt                  >  2:153476/1‑140 (MQ=255)                                                                                                             aTCCTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACtt                  >  1:316605/1‑140 (MQ=255)                                                                                                               ccTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTa                <  2:369158/140‑1 (MQ=255)                                                                                                                cTAAGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc               <  2:316605/140‑1 (MQ=255)                                                                                                                  aaGGATTATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACgg             <  2:191427/140‑1 (MQ=255)                                                                                                                        tATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc               <  2:342586/132‑1 (MQ=255)                                                                                                                        tATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc               >  1:342586/1‑132 (MQ=255)                                                                                                                        tATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGt       >  2:285990/1‑140 (MQ=255)                                                                                                                        tATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGt       >  2:133799/1‑140 (MQ=255)                                                                                                                        tATCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGt       >  1:221341/1‑140 (MQ=255)                                                                                                                         aTCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCACAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTa      >  1:305902/1‑140 (MQ=255)                                                                                                                          tCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTaa     >  2:38708/1‑140 (MQ=255)                                                                                                                          tCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTaa     >  2:429443/1‑140 (MQ=255)                                                                                                                          tCCGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTaa     >  2:480413/1‑140 (MQ=255)                                                                                                                            cGAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGt   <  1:480413/140‑1 (MQ=255)                                                                                                                             gAAAAATAATCCCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTc  >  2:147712/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                  CCGTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTC  >  NC_000913/2023592‑2023855

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: ‑