Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,023,730	A→G	intergenic (+52/‑238)	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	2,023,730	0	A	G	100.0%	169.0 / NA	49	intergenic (+52/‑238)	fliR/rcsA	flagellar biosynthesis protein FliR/DNA‑binding transcriptional activator RcsA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (32/17);  total (32/17)

GTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAA  >  NC_000913/2023594‑2023865                                                                                                                                         |                                                                                                                                        gTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCAGGTTATCCGAAGGATTATCCGAGAAATAATACCTGCGa                                                                                                                                      >  1:192213/1‑140 (MQ=255) gTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCAAGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGa                                                                                                                                      >  1:233788/1‑140 (MQ=255)          aCCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATTATGTTATCATAAGGATTATCCGAAAGATAAAACCTGCGAACATCTTcc                                                                                                                             >  2:260474/1‑140 (MQ=255)              ttttGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGACTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCa                                                                                                                            <  1:155243/137‑1 (MQ=255)              ttttGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGACTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCa                                                                                                                            >  2:155243/1‑137 (MQ=255)               tttGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAAGAAAACCTGCTAACATCTTCCAGGAt                                                                                                                        >  1:278383/1‑140 (MQ=255)                                 gTGAAATTTTTAATTTGCTGGCTGATATTTTTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAatat                                                                                                      <  1:270745/140‑1 (MQ=255)                                  tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATAtt                                                                                                     >  2:146686/1‑140 (MQ=255)                                  tGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCCGCGAACACCTTGCAAGATACTCCTGCAGCGAAATAtt                                                                                                     >  1:273305/1‑140 (MQ=255)                                    aaaTTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTg                                                                                                   >  2:560040/1‑140 (MQ=255)                                         tttAATTTGCTGGCTGGTATTAATAGTGAATTGACTTTATTATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTa                                                                                              <  2:305029/140‑1 (MQ=255)                                           aaaTTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAg                                                                                            <  1:545868/139‑1 (MQ=255)                                             aTTTGCTGGCTGATATTCTTAGTGAATTGCCCTTAATATCATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGct                                                                                          <  2:225349/140‑1 (MQ=255)                                                 gctggctgATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGctcact                                                                                      <  2:374345/140‑1 (MQ=255)                                                                   tGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGGAATCTTTGTTTTAAGCTCACTGACATATCGCAACAttta                                                                    >  2:210491/1‑140 (MQ=255)                                                                   tGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTATGCGCACTCATATATCGCAACAttta                                                                    >  1:219705/1‑140 (MQ=255)                                                                   tGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAttta                                                                    >  2:472066/1‑140 (MQ=255)                                                                      aTTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactt                                                                 <  1:560040/140‑1 (MQ=255)                                                                      aTTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAAGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttactt                                                                 <  1:423633/140‑1 (MQ=255)                                                                       ttGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACAtttacttt                                                                >  2:73869/1‑140 (MQ=255)                                                                                    aaTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAAt                                                   >  1:30222/1‑140 (MQ=255)                                                                                     aTTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAAtt                                                  >  2:442223/1‑140 (MQ=255)                                                                                         cGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAg                                              >  2:561906/1‑140 (MQ=255)                                                                                         cGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAg                                              <  1:146686/140‑1 (MQ=255)                                                                                           tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGc                                            >  2:123809/1‑140 (MQ=255)                                                                                           tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGc                                            >  2:390645/1‑140 (MQ=255)                                                                                           tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGc                                            >  1:591620/1‑140 (MQ=255)                                                                                           tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGc                                            >  2:299987/1‑140 (MQ=255)                                                                                           tAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTGAAGACAATTCCAGGc                                            >  1:226925/1‑140 (MQ=255)                                                                                                   aTCATGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATtata                                    <  1:390645/140‑1 (MQ=255)                                                                                                      aTGTTATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATacaa                                 <  2:591620/140‑1 (MQ=255)                                                                                                        cagaTCCTAAGGATTATCCGAAAAATAATACTTGCTAACATCTTCCAGAATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATacaaca                               <  2:230699/137‑1 (MQ=255)                                                                                                          tATCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACt                             >  2:138460/1‑140 (MQ=255)                                                                                                            tCCTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACttt                           >  2:36591/1‑140 (MQ=255)                                                                                                              cTAAGGATTATCCGAAAAATAATACCTGCGAACATTTTCTAGGATACTACTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc                         <  2:278383/140‑1 (MQ=255)                                                                                                              cTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc                         <  1:455500/140‑1 (MQ=255)                                                                                                              cTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc                         >  1:107148/1‑140 (MQ=255)                                                                                                              cTAAGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTAc                         <  2:9357/140‑1 (MQ=255)                                                                                                                aaGGATTATCCGAAAAATAATAGCTGCGAACATCTACCAGGATACTCCAGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACgg                       <  2:273305/140‑1 (MQ=255)                                                                                                                aaGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACgg                       >  2:642646/1‑140 (MQ=255)                                                                                                                 aGGATTATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACggg                      >  2:231816/1‑140 (MQ=255)                                                                                                                      tATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGATAATTCCAGGCAGATTATACAATACTTTACGGGATAGt                 >  1:179351/1‑140 (MQ=255)                                                                                                                      tATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCATATTATACAAAACTTTACGGGAtctg                 >  1:230699/1‑137 (MQ=255)                                                                                                                      tATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGt                 >  2:393371/1‑140 (MQ=255)                                                                                                                      tATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGt                 >  1:30769/1‑140 (MQ=255)                                                                                                                      tATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGt                 >  2:663730/1‑140 (MQ=255)                                                                                                                      tATCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAACACATTTCCAGGCAAATCATACAACACTTTACGGGATAGt                 >  2:245725/1‑140 (MQ=255)                                                                                                                        tCCGAAAAATAATACCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTaa               >  1:68626/1‑140 (MQ=255)                                                                                                                                  aataCCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACGATTCCAGGAAAATTATACAACACTTGACGGGATAGTAAGTCCGCCTGa     >  2:174417/1‑140 (MQ=255)                                                                                                                                     aCCTGCGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGaaaa  <  1:642646/140‑1 (MQ=255)                                                                                                                                         |                                                                                                                                        GTTAATTGCACCTTTTTGCGAACATTTATTCAGTGAAATTTTTAATTTGCTGGCTGATATTATTAGTGAATTGCCATTAATATAATTCCGTAACGTTTATCATGTTATCCTAAGGATTATCCGAAAAATAATACCTACGAACATCTTCCAGGATACTCCTGCAGCGAAATATTTGTTTTAAGCTCACTCACATATCGCAACATTTACTTTACTTTAAGACAATTCCAGGCAAATTATACAACACTTTACGGGATAGTAAGTCCGCCTGAAAA  >  NC_000913/2023594‑2023865

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: ‑