Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,593,447	T→C	S52P (TCC→CCC)	yjjQ →	response regulator transcription factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,593,447	0	T	C	100.0%	232.4 / NA	66	S52P (TCC→CCC)	yjjQ	response regulator transcription factor
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (44/22);  total (44/22)

AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACA  >  NZ_CP009273/4593364‑4593529                                                                                    |                                                                                   agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:865307/1‑90 (MQ=255) agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:411664/1‑90 (MQ=255) agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:106584/1‑90 (MQ=255) agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:615024/1‑90 (MQ=255) agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:1223723/1‑90 (MQ=255) agGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:1193744/1‑90 (MQ=255)  ggTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAtt                                                                             >  2:952194/1‑90 (MQ=255)            aCTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCt                                                                   >  1:999913/1‑90 (MQ=255)            aCTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCt                                                                   >  2:221829/1‑90 (MQ=255)             cTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTg                                                                  >  2:964371/1‑90 (MQ=255)                       tGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCgg                                                        >  2:723032/1‑90 (MQ=255)                           tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa                                                    <  1:463241/90‑1 (MQ=255)                           tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa                                                    >  1:515760/1‑90 (MQ=255)                           tatGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGaa                                                    <  2:907583/90‑1 (MQ=255)                              gAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              >  2:747547/1‑61 (MQ=255)                              gAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGAt                                                                              <  1:747547/61‑1 (MQ=255)                              gAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGt                                                 >  1:43909/1‑90 (MQ=255)                                aataatATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGa                                               <  1:723134/90‑1 (MQ=255)                                  taataTCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAg                                             >  2:1172275/1‑90 (MQ=255)                                  taataTCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAg                                             >  2:779002/1‑90 (MQ=255)                                     tatCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATc                                          <  2:701406/90‑1 (MQ=255)                                         cAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACg                                      >  1:740176/1‑90 (MQ=255)                                         cAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACg                                      >  1:247656/1‑90 (MQ=255)                                         cAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACg                                      >  2:520642/1‑90 (MQ=255)                                         cAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACg                                      >  2:82722/1‑90 (MQ=255)                                           gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt                                    >  2:1185904/1‑90 (MQ=255)                                           gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt                                    >  1:52484/1‑90 (MQ=255)                                           gcgcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGtt                                    >  2:704627/1‑90 (MQ=255)                                             gcCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCt                                  <  2:52484/90‑1 (MQ=255)                                              ccTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTg                                 >  1:638363/1‑90 (MQ=255)                                                tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGAtt                                                               >  1:1190766/1‑58 (MQ=255)                                                tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGAtt                                                               <  2:1190766/58‑1 (MQ=255)                                                tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGt                                     <  1:455718/84‑1 (MQ=255)                                                tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGt                                     >  2:455718/1‑84 (MQ=255)                                                tctGCGGAGGACCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGtt                               >  2:52127/1‑90 (MQ=255)                                                     ggaggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGa                          <  2:999913/90‑1 (MQ=255)                                                     ggaggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGa                          <  2:961968/90‑1 (MQ=255)                                                     ggaggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGa                          <  2:32254/90‑1 (MQ=255)                                                     ggaggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGa                          <  2:309958/90‑1 (MQ=255)                                                       aggaCCTTACCTTATTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAAc                        <  2:592358/90‑1 (MQ=255)                                                           ccttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACatta                    >  1:903783/1‑90 (MQ=255)                                                             ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt                  >  2:245812/1‑90 (MQ=255)                                                             ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt                  >  1:140729/1‑90 (MQ=255)                                                             ttaccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatt                  >  1:838260/1‑90 (MQ=255)                                                              taccttaTTACAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACattatta                 <  2:686704/90‑1 (MQ=255)                                                                  ttattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCt             >  1:247476/1‑90 (MQ=255)                                                                  ttattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCt             >  1:321258/1‑90 (MQ=255)                                                                  ttattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCt             >  1:678877/1‑90 (MQ=255)                                                                   tattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCtt            <  1:1223723/90‑1 (MQ=255)                                                                   tattaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCtt            >  2:490989/1‑90 (MQ=255)                                                                    attaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATcc                                         >  1:817021/1‑60 (MQ=255)                                                                    attaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATcc                                         <  2:817021/60‑1 (MQ=255)                                                                    attaCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCttt           >  2:487050/1‑90 (MQ=255)                                                                       aCAATTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAt        <  1:490989/90‑1 (MQ=255)                                                                          aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc     >  2:131060/1‑90 (MQ=255)                                                                          aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc     >  2:410587/1‑90 (MQ=255)                                                                          aTTACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAAtctc     >  2:350762/1‑90 (MQ=255)                                                                            tACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTcac   <  2:247476/90‑1 (MQ=255)                                                                            tACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTcac   <  1:1193744/90‑1 (MQ=255)                                                                            tACGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTcac   <  1:964371/90‑1 (MQ=255)                                                                             aCGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAg                                             <  1:474815/47‑1 (MQ=255)                                                                             aCGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAg                                             >  2:474815/1‑47 (MQ=255)                                                                             aCGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTcaca  >  1:304381/1‑90 (MQ=255)                                                                             aCGTCGTCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACAGTATTATTCTTTAATCTcaca  >  2:1176988/1‑90 (MQ=255)                                                                              cgtcgtCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCAc                                       >  2:1068627/1‑52 (MQ=255)                                                                              cgtcgtCCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCAc                                       <  1:1068627/52‑1 (MQ=255)                                                                                    |                                                                                   AGGTCATGAGGACTCACTTCCCTGAATATGAAATAATATCCAGCGCCTCTGCGGAGGACCTTACCTTATTACAATTACGTCGTTCCGGATTAGTCATTGCTGATTTAGCCGGTGAAAGTGAAGATCCACGTTCTGTTTGTGAACATTATTATTCTTTAATCTCACA  >  NZ_CP009273/4593364‑4593529

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑