Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,587,586	C→A	intergenic (+155/‑9)	narQ → / → acrD	sensory histidine kinase NarQ/multidrug efflux pump RND permease AcrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,587,586	0	C	A	100.0%	118.8 / NA	36	intergenic (+155/‑9)	narQ/acrD	sensory histidine kinase NarQ/multidrug efflux pump RND permease AcrD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (23/13);  total (23/13)

CTTAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACC  >  NC_000913/2587461‑2587716                                                                                                                              |                                                                                                                                   cTTAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCg                                                                                                                      >  2:519719/1‑140 (MQ=255)   tAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGaa                                                                                                                    >  1:383763/1‑140 (MQ=255)    aaGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAAt                                                                                                                   >  2:152854/1‑140 (MQ=255)    aaGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAAt                                                                                                                   >  2:602579/1‑140 (MQ=255)              ataAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTg                                                                                                         >  2:748318/1‑140 (MQ=255)                  aaGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCg                                                                                                     >  1:394230/1‑140 (MQ=255)                    gggCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGcc                                                                                                   <  2:289922/140‑1 (MQ=255)                       cATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCa                                                                                                >  1:286956/1‑140 (MQ=255)                       cATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCa                                                                                                >  2:683490/1‑140 (MQ=255)                       cATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCa                                                                                                >  1:197807/1‑140 (MQ=255)                                    aTTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGt                                                                                   >  1:412366/1‑140 (MQ=255)                                      tAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGATACAGTGAACCAAGTCAAGCCTACAACGTTACGCAGAAAAACGAGGGACTCTTTTAATGGCGAATTTCTTTATTGATCCCCCCATTTTTGCCAgggatt                                                                                 >  2:353696/1‑137 (MQ=255)                                      aaaCTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGc                                                                                 >  1:622780/2‑140 (MQ=255)                                        aCTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTg                                                                               >  1:378460/1‑140 (MQ=255)                                          tCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGc                                                                             >  1:579145/1‑140 (MQ=255)                                            cTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCaa                                                                           <  1:602579/140‑1 (MQ=255)                                              ttttttCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATc                                                                         <  2:246707/140‑1 (MQ=255)                                                       cACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTgtgt                                                                <  2:197807/140‑1 (MQ=255)                                                            ttGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGAc                                                           <  2:734294/140‑1 (MQ=255)                                                               gCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAgg                                                        >  1:196181/1‑140 (MQ=255)                                                                    tACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTAccc                                                   >  1:170342/1‑140 (MQ=255)                                                                    tACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTAccc                                                   >  1:609479/1‑140 (MQ=255)                                                                       cTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTgg                                                <  2:378460/140‑1 (MQ=255)                                                                       cTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTgg                                                <  2:622780/140‑1 (MQ=255)                                                                          gCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGa                                             >  1:97652/1‑140 (MQ=255)                                                                          gCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGa                                             >  1:91564/1‑140 (MQ=255)                                                                                    tGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCAtt                                   <  1:707097/140‑1 (MQ=255)                                                                                           aGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGtt                            <  1:480087/140‑1 (MQ=255)                                                                                           aGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGtt                            <  1:467320/140‑1 (MQ=255)                                                                                           aGTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGtt                            >  1:105143/1‑140 (MQ=255)                                                                                            gTCAAGCCTACAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTg                           <  2:609479/140‑1 (MQ=255)                                                                                                      cAACGATACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATAccc                 >  1:21339/1‑140 (MQ=255)                                                                                                           aTACGCAGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGAtc            >  2:260591/1‑140 (MQ=255)                                                                                                            tACGCAGAAACACGAGGTACTCTTTTAATGACGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGAtct           >  1:664328/1‑140 (MQ=255)                                                                                                                 aGAAACACGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCgcgc      >  2:389817/1‑140 (MQ=255)                                                                                                                     acacGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCAcc  <  2:269566/140‑1 (MQ=255)                                                                                                                     acacGAGGTACTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCAcc  <  2:286956/140‑1 (MQ=255)                                                                                                                              |                                                                                                                                   CTTAAGGTTCAGTATAAAAGGGCATGATAATTTACATTAACTCCTTTTTTTCTCCACGATTGGCTCGTACCTTGCCGCTACAGTGAAGCAAGTCAAGCCTACAACGATACGCAGAAACACGAGGTCCTCTTTTAATGGCGAATTTCTTTATTGATCGCCCCATTTTTGCCTGGGTGCTGGCAATCCTGTTGTGTCTGACAGGTACCCTGGCGATTTTTTCATTGCCCGTTGAACAATACCCCGATCTCGCGCCACC  >  NC_000913/2587461‑2587716

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑