Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,594,535	T→C	intergenic (‑69/+10)	lsrK ← / ← lsrR	autoinducer‑2 kinase/transcriptional regulator LsrR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,594,535	0	T	C	100.0%	159.9 / NA	42	intergenic (‑69/+10)	lsrK/lsrR	autoinducer‑2 kinase/transcriptional regulator LsrR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (26/16);  total (26/16)

GGTAAAGAGTCGAGCCATTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGTCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATAACCGCCTTTCATTGCAGC  >  NZ_CP009273/1594449‑1594619                                                                                       |                                                                                     ggTAAAGAGTCGAGCCATTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATg                                                                                  <  2:861201/91‑1 (MQ=255)    aaaGAGTCGAGCCATTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCaa                                                                               >  2:845441/1‑91 (MQ=255)         gTCGAGCCATTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTa                                                                          >  1:191832/1‑91 (MQ=255)          tCGAGCCATTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTaa                                                                         >  2:269007/1‑91 (MQ=255)                 aTTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTa                                                                  >  2:764201/1‑91 (MQ=255)                      aTTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATc                                                             <  2:89422/91‑1 (MQ=255)                          tCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATcgccg                                                         >  1:404369/1‑91 (MQ=255)                           ccTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTTTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATcgccgc                                                        >  2:648148/1‑91 (MQ=255)                           ccTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATcgccgc                                                        <  2:351795/91‑1 (MQ=255)                           ccTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATcgccgc                                                        <  1:764201/91‑1 (MQ=255)                           ccTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATcgccgc                                                        >  1:327539/1‑91 (MQ=255)                                gCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGctgctg                                                   <  1:78751/91‑1 (MQ=255)                                     tGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTcc                                              <  1:704959/91‑1 (MQ=255)                                       cGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTg                                            <  1:718534/91‑1 (MQ=255)                                         ttCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGAt                                          <  1:538988/91‑1 (MQ=255)                                         ttCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGAt                                          <  2:404369/91‑1 (MQ=255)                                         ttCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGAt                                          >  2:538988/1‑91 (MQ=255)                                          tctgtctgTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATc                                         >  2:27433/1‑91 (MQ=255)                                             gtctgtTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTACCTACGTAAAATCGGCGCTGCTGTGTCCTGATCGGt                                      >  2:22330/1‑91 (MQ=255)                                             gtctgtTCCTCTATACGTTATCCATAATTCCCGGAAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGt                                      >  2:313495/1‑91 (MQ=255)                                              tctgtTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTa                                     <  1:2380/91‑1 (MQ=255)                                                   tCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAg                                <  1:568818/91‑1 (MQ=255)                                                   tCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAg                                <  2:385094/91‑1 (MQ=255)                                                    ccTCTATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGt                               <  1:660738/91‑1 (MQ=255)                                                       ctATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCg                            >  2:303691/1‑91 (MQ=255)                                                       ctATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCg                            >  1:397439/1‑91 (MQ=255)                                                       ctATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCg                            >  2:808054/1‑91 (MQ=255)                                                       ctATACGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCg                            >  1:319954/1‑91 (MQ=255)                                                         ataCGTTCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGtt                          <  1:27433/91‑1 (MQ=255)                                                              ttCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGatat                     >  2:299939/1‑91 (MQ=255)                                                              ttCTCCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGatat                     >  2:362383/1‑91 (MQ=255)                                                                ctcCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTaaaa                                                               >  2:342482/1‑47 (MQ=255)                                                                ctcCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTaaaa                                                               <  1:342482/47‑1 (MQ=255)                                                                ctcCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATaa                   >  2:112157/1‑91 (MQ=255)                                                                ctcCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATaa                   >  1:247868/1‑91 (MQ=255)                                                                ctcCATCATTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATaa                   >  2:359733/1‑91 (MQ=255)                                                                   catcatTCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATAACCg                >  2:761542/1‑91 (MQ=255)                                                                        ttCCCGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATAACCGCCttt           >  1:425316/1‑91 (MQ=255)                                                                            cGGTAATAAGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATAACCGCCTTTCAtt       >  1:362133/1‑91 (MQ=255)                                                                                 ataaGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATAACCGCCTTTCATTGCAGc  >  1:827422/1‑91 (MQ=255)                                                                                   aaGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTgtgt                                                <  1:361003/43‑1 (MQ=255)                                                                                   aaGGCCATGCAAATTTAACTACGTAAAATCGCCGCTGCTgtgt                                                >  2:361003/1‑43 (MQ=255)                                                                                       |                                                                                     GGTAAAGAGTCGAGCCATTAGATTATCCTCGGCTTATGCGTTCTGTCTGTTCCTCTATACGTTCTCCATCATTCCCGGTAATAAGGTCATGCAAATTTAACTACGTAAAATCGCCGCTGCTGTGTCCTGATCGGTAACCAGTGCGTTGATATAACCGCCTTTCATTGCAGC  >  NZ_CP009273/1594449‑1594619

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑