Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	481,730	Δ1 bp	coding (514/648 nt)	acrR →	multidrug efflux transporter transcriptional repressor AcrR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	481,728	0	T	.	100.0%	175.1 / NA	40	coding (512/648 nt)	acrR	multidrug efflux transporter transcriptional repressor AcrR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (20/20);  total (20/20)

TCTCTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAAT  >  NZ_CP009273/481612‑481862                                                                                                                     |                                                                                                                                       tctcTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGc                                                                                                                 >  1:359232/1‑139 (MQ=255)      gtctgGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCttt                                                                                                            >  1:831993/1‑139 (MQ=255)            aaaGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCg                                                                                                      <  1:461687/139‑1 (MQ=255)             aaGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGc                                                                                                     <  1:274576/139‑1 (MQ=255)              aGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCa                                                                                                    <  1:479468/139‑1 (MQ=255)               gTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCaa                                                                                                   >  1:328965/1‑139 (MQ=255)                         tataGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATc                                                                                         >  1:249158/1‑139 (MQ=255)                          ataGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGa                                                                                                                         >  2:459268/1‑106 (MQ=255)                          ataGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGa                                                                                                                         <  1:459268/106‑1 (MQ=255)                                  aaCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAaag                                                                                <  1:222228/139‑1 (MQ=255)                                   aCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAaag                                                                                >  2:242238/1‑138 (MQ=255)                                   aCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAaag                                                                                >  2:235982/1‑138 (MQ=255)                                   aCGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAaag                                                                                >  2:222228/1‑138 (MQ=255)                                                 tATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACg                                                                 >  2:285203/1‑139 (MQ=255)                                                 tATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACg                                                                 >  2:721015/1‑139 (MQ=255)                                                      aaGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCTGCTATTACTTTGc                                                             <  2:465094/138‑1 (MQ=255)                                                          gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt                                                        <  1:235982/139‑1 (MQ=255)                                                          gAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCt                                                        <  1:376411/139‑1 (MQ=255)                                                           aaaaTGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCAt                                                          <  1:737465/136‑1 (MQ=255)                                                           aaaaTGTTGCCTGCGGATTTAATGAAGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCAt                                                          >  2:737465/1‑136 (MQ=255)                                                                 ttGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGga                                                 <  2:644204/139‑1 (MQ=255)                                                                        cGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGt                                            <  2:831993/137‑1 (MQ=255)                                                                        cGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGt                                            <  2:249158/137‑1 (MQ=255)                                                                                    cgcgTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGccc                               >  2:703981/1‑138 (MQ=255)                                                                                     gcggcgGGCAGCAATTATTAATCGGGGCTATA‑ATCCGGGCTGGTGGAAAACTTGCTCTTTGCCCCCCAAACTTTTGGACCTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCa                             <  1:517672/139‑1 (MQ=255)                                                                                       gTCGCGCAGCAATTATTATGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACg                           <  1:275392/139‑1 (MQ=255)                                                                                                   ttattaTGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTa                    <  1:280621/134‑1 (MQ=255)                                                                                                   ttattaTGCGCGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTa                    >  2:280621/1‑134 (MQ=255)                                                                                                          gcgcGGCTATA‑TTCCGGCCTGCTGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACt         >  2:845792/1‑138 (MQ=255)                                                                                                          gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCt                                                                                        >  2:603367/1‑59 (MQ=255)                                                                                                          gcgcGGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCt                                                                                        <  1:603367/59‑1 (MQ=255)                                                                                                           cgcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGc                                                             <  2:140712/85‑1 (MQ=255)                                                                                                           cgcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGc                                                             >  1:140712/1‑85 (MQ=255)                                                                                                           cgcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCt                                     <  2:621912/109‑1 (MQ=255)                                                                                                           cgcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCt                                     >  1:621912/1‑109 (MQ=255)                                                                                                           cgcgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTaa       >  2:278046/1‑139 (MQ=255)                                                                                                             cgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTa        <  2:252454/136‑1 (MQ=255)                                                                                                             cgGCTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTa        >  1:252454/1‑136 (MQ=255)                                                                                                                cTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGaa   >  1:247717/1‑138 (MQ=255)                                                                                                                cTATA‑TTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAAt  <  2:328965/139‑1 (MQ=255)                                                                                                                     |                                                                                                                                       TCTCTGTCTGGAAAGTTATGACCGTATAGAACAAACGTTAAAACATTGTATTGAAGCGAAAATGTTGCCTGCGGATTTAATGACGCGTCGCGCAGCAATTATTATGCGCGGCTATATTTCCGGCCTGATGGAAAACTGGCTCTTTGCCCCGCAATCTTTTGATCTTAAAAAAGAAGCCCGCGATTACGTTGCCATCTTACTGGAGATGTATCTCCTGTGCCCCACGCTTCGTAATCCTGCCACTAACGAAT  >  NZ_CP009273/481612‑481862

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑