Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,982,555	T→C	F232S (TTC→TCC)	yqeI →	transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,982,555	0	T	C	100.0%	130.3 / NA	37	F232S (TTC→TCC)	yqeI	transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/22);  total (15/22)

AATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC  >  NZ_CP009273/2982469‑2982641                                                                                       |                                                                                       aaTTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTcccc                                                                                     >  1:236964/1‑90 (MQ=255)     gATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCtt                                                                                 >  1:589853/1‑90 (MQ=255)      aTGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTg                                                                                >  1:831390/1‑90 (MQ=255)          gTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCaaa                                                                            >  1:792678/1‑90 (MQ=255)              aaaGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATcc                                                                        <  2:182551/90‑1 (MQ=255)                agagTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTc                                                                      <  2:453757/90‑1 (MQ=255)                  agTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAc                                                                    <  1:619741/90‑1 (MQ=255)                   gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc                                                                   >  1:154655/1‑90 (MQ=255)                   gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc                                                                   >  1:345989/1‑90 (MQ=255)                   gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc                                                                   >  2:762165/1‑90 (MQ=255)                   gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc                                                                   >  1:501501/1‑90 (MQ=255)                   gTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCAcc                                                                   <  1:55879/90‑1 (MQ=255)                     tCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCgg                                                                 <  1:40599/90‑1 (MQ=255)                          aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg                                                            <  2:773815/90‑1 (MQ=255)                          aaaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg                                                            <  2:373306/90‑1 (MQ=255)                           aaTATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatga                                                           <  2:97393/90‑1 (MQ=255)                                 aaaCACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTa                                                     >  1:99275/1‑90 (MQ=255)                                      cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa                                                >  1:872985/1‑90 (MQ=255)                                      cGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCa                                                >  2:670308/1‑90 (MQ=255)                                       ggATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCAt                                               <  1:361755/90‑1 (MQ=255)                                          tACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCa                                            <  2:579896/90‑1 (MQ=255)                                               gATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaaa                                       <  2:157781/90‑1 (MQ=255)                                               gATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaaa                                       <  1:402124/90‑1 (MQ=255)                                                aTTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATaaaa                                      <  1:397690/90‑1 (MQ=255)                                                    ggggATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACta                                  >  1:264060/1‑90 (MQ=255)                                                       gATTAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATaa                               <  2:84401/90‑1 (MQ=255)                                                          tAACTGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCa                            >  2:430192/1‑90 (MQ=255)                                                              tGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg                                                            >  2:553390/1‑54 (MQ=255)                                                              tGTAAAAAACATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg                                                            <  1:553390/54‑1 (MQ=255)                                                                       cATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg                                                            <  1:400495/45‑1 (MQ=255)                                                                       cATCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGgatg                                                            >  2:400495/1‑45 (MQ=255)                                                                        aTCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaa              <  1:670308/90‑1 (MQ=255)                                                                         tCCGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCaaa             >  1:533401/1‑90 (MQ=255)                                                                          ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc            <  2:165250/90‑1 (MQ=255)                                                                          ccGTGGTTATACTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc            <  2:792678/90‑1 (MQ=255)                                                                          ccGTGGTTATACTCCCCTCATGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAAc            <  2:668955/90‑1 (MQ=255)                                                                                    aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc  <  1:430192/90‑1 (MQ=255)                                                                                    aCTCCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAAccc  <  1:880420/90‑1 (MQ=255)                                                                                       |                                                                                       AATTGATGGGTTGAAAGAGTTCGATAAATATAAAACACGGATACTGGATTCGGGGATTAACTGTAAAAAACATCCGTGGTTATACTTCCCTCTTGCAAAATCCTCACCGGGGATGATTGTTATGGCATGCAATAAAAACTATAACCAACATGAAGTGGCAAACTGTTTAACCC  >  NZ_CP009273/2982469‑2982641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑