Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,249,979	T→G	P102P (CCT→CCG)	unknown →	Two‑component system response regulator QseB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,249,979	0	T	G	100.0%	95.9 / NA	34	P102P (CCT→CCG)	unknown	Two‑component system response regulator QseB
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (19/15);  total (19/15)

TTCGCCGTGGATTGGTTTACCGACGGCAAAACCGGATTGGAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCTTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGGACACGCCAAGACAATGACTAAATATTTCGCTTATGACG  >  1/1249746‑1250073                                                                                                                                                                                                                                          |                                                                                               ttCGCCGTGGATTGGTTTACCGACGGCAAAACCGGATTGGAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAgt                                                                               <  1:355023/251‑1 (MQ=255)     ccGTGGATTGGTTTACCGACGGCAAAACCGGATTGGAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAgtggtg                                                                           <  1:277494/251‑1 (MQ=255)          gATTGGTTTACCGACGGCAAAACCGGATTGGAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACg                                                                      >  1:409930/1‑251 (MQ=255)                       aCGGCAAAACCGGATTGGAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTg                                                         <  1:416297/251‑1 (MQ=255)                                        gAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACga                                        >  1:511051/1‑250 (MQ=255)                                         aaGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACga                                        <  1:219130/250‑2 (MQ=255)                                                   gTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaa                             >  1:247782/1‑249 (MQ=255)                                                    tCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            <  1:417059/251‑4 (MQ=255)                                                         gcCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            <  1:622448/246‑4 (MQ=255)                                                          ccTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGAtt                                                      <  1:759377/219‑1 (MQ=255)                                                          ccTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactca                      >  1:240970/1‑247 (MQ=255)                                                            ttATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCGCGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaa                    >  1:307522/1‑245 (MQ=255)                                                              atgatgCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacc                  <  1:216295/251‑9 (MQ=255)                                                              atgatgCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacc                  <  1:360084/251‑9 (MQ=255)                                                                 atgCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            >  1:885267/1‑235 (MQ=255)                                                                 atgCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctg                >  1:767548/1‑240 (MQ=255)                                                                     aGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            >  1:645417/1‑231 (MQ=255)                                                                         gtgCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            >  1:151682/1‑227 (MQ=255)                                                                         gtgCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctgctgcacgcg       >  1:823060/1‑232 (MQ=255)                                                                              ggATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            >  1:200766/1‑222 (MQ=255)                                                                              ggATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctgctgcacgcgttatt  >  1:92928/1‑227 (MQ=255)                                                                              ggATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGCTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctgctgcacgcgttatt  >  1:733880/1‑227 (MQ=255)                                                                               gATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAg                                                               <  1:417957/189‑1 (MQ=255)                                                                               gATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTgt                                                   >  1:367974/1‑201 (MQ=255)                                                                               gATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactc                       >  1:697391/1‑226 (MQ=255)                                                                                aTTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAgt                                                                               >  1:752323/1‑172 (MQ=255)                                                                                          gCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctgctgcacgcg       <  1:486797/234‑20 (MQ=255)                                                                                              aaaaTGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAgt                                                                               <  1:111605/158‑1 (MQ=255)                                                                                                            ggATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGTTGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAgt                                                                               >  1:152341/1‑144 (MQ=255)                                                                                                                  gtTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctgctgcacgcg       >  1:473220/1‑191 (MQ=255)                                                                                                                                         ggCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCaaaac                            <  1:335331/166‑4 (MQ=255)                                                                                                                                                            gATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGAACACGCCAAAACaactcaaacctgctg             >  1:404328/1‑149 (MQ=255)                                                                                                                                                                                ctctGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCGTTTGCCCTGGCGGAAGTGGTGGCa                                                                        <  1:221465/83‑1 (MQ=255)                                                                                                                                                                                  ctGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTTTTTGTGTAAGCCGTTTGTCCTGGCGGAAGTGGTGGCa                                                                        <  1:237339/81‑1 (MQ=255)                                                                                                                                                                                                                                          |                                                                                               TTCGCCGTGGATTGGTTTACCGACGGCAAAACCGGATTGGAAGCGGCGCAGTCGGCGCCTTATGATGCAGTGGTGCTGGATTTAACCTTGCCGAAAATGGACGGGCTGGATGTGTTGCAGGCATGGCGTAAAAACGGGCAGGATGTGCCGGTGCTGATTCTTACCGCGCGGGATACTCTGGATGAGCGCATTACCGGCTTGCAACGCGGTGCGGACGATTATTTGTGTAAGCCTTTTGCCCTGGCGGAAGTGGTGGCACGTTTGCAGGCACTGATTTGTCGTCGCTACGGACACGCCAAGACAATGACTAAATATTTCGCTTATGACG  >  1/1249746‑1250073

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑