Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,797,772	G→C	100%	R7G (CGC→GGC)	phoR ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,797,772	0	G	C	100.0%	119.4 / NA	44	R7G (CGC→GGC)	phoR	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (21/23);  total (21/23)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797637‑1797908                                                                                                                                        |                                                                                                                                         aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCcgtgg                                                                                                                                      <  1:609182/140‑1 (MQ=255) aaataTATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAACCcgtgg                                                                                                                                      >  1:120836/1‑140 (MQ=255)        tGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATTTACTGCTAATCAATAACATTAAGAggcggataagat                                                                                                                               >  2:326558/1‑133 (MQ=255)         gATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACtt                                                                                                                              >  2:69433/1‑140 (MQ=255)          aTCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGCGGTGAAAGTtc                                                                                                                             >  1:695250/1‑140 (MQ=255)           tCTTGCATCTGTTGCTAGAGCTTGTTCATGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTtca                                                                                                                            >  2:581562/1‑140 (MQ=255)              tGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATCTGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGATTATCAATAACATTAAGCCGTCGTGAAACTtcatca                                                                                                                         >  2:397489/1‑140 (MQ=255)                  tCTGTTGCTAGATCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGt                                                                                                                     <  2:404203/140‑1 (MQ=255)                  tCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACATCATCATTGt                                                                                                                     >  1:80364/1‑140 (MQ=255)                   cTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGtt                                                                                                                    >  2:439358/1‑140 (MQ=255)                    tGTTGCTAGAGCTTGTTCGTG‑TTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCt                                                                                                                  >  1:215875/1‑140 (MQ=255)                      ttGCTAGAGCTTGTTCGGGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATACCATTAAGCCGTGGTGAAACTTCTTCATTGTTCtt                                                                                                                 <  2:373633/140‑1 (MQ=255)                           agtgCTTGTTCGTGTTTTTCTGATAAAAAATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAAATAAAATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGt                                                                                                            <  1:137311/137‑1 (MQ=255)                           agagCTTGTTCGTGTTTTTCTGATAAAACACCAGAGATGGACAACTGAAAAATAATACATACTGTAACAAAAATAAAAATTAAAATATCACAAAAACAAAACATAAAGCCACGCTTATACTTCATCATTTTTCTTTAGGt                                                                                                            >  2:604825/1‑140 (MQ=255)                           agagCTTGTTCATGTTTTTCTGATACGACTTGAATGATGCAGGCGTGAATAATAATGACTAATGTAACAAAACTGATAATTAATATACTGCTTATAACTCACATTAAGCCGTGGTGACACTTCATCATTGTCGTTTAgta                                                                                                            >  2:123178/1‑138 (MQ=255)                              gcttttgcttggttttCTTATAAAACATACGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAATACTGATAATTAATATACTTCTCATCAATAATATTAAGCCGTGGTGAAACTTCATTATTGTTCTTTCGGTCtt                                                                                                         <  2:376497/128‑1 (MQ=255)                              gCTTGTTCGTGTTTTTTTGTTTTATCTTATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTCCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCtt                                                                                                         >  2:205761/1‑140 (MQ=255)                               cTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCttt                                                                                                        >  2:638770/1‑140 (MQ=255)                               cTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGCGGAAAGATAATCATTGTTATGAAGGTCgtt                                                                                                        >  2:567546/1‑140 (MQ=255)                                  gTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAATGTTCTTTAGGTCTTTCCa                                                                                                     >  1:85764/1‑140 (MQ=255)                                     cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAtt                                                                                                  >  2:129914/1‑140 (MQ=255)                                          ttttCTGATAAATCCCATGTGTCGGAAGTGTTAATAATAATGCCTAATGTAACAAAACTGATTATTAATATTCTGCTTATCAATAACATTAATCCGTGGTGATTTTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAg                                                                                             <  2:20786/140‑1 (MQ=255)                                          ttttCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAg                                                                                             <  1:112953/140‑1 (MQ=255)                                             tCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAAATGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCt                                                                                          >  1:137843/1‑140 (MQ=255)                                             tCTGATAAAACATATGTGATGGAAGCGTGAACAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATATCCt                                                                                          >  1:126117/1‑140 (MQ=255)                                               tGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAACCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTaa                                                                                        >  1:252035/1‑140 (MQ=255)                                                       cATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGca                                                                                <  2:268426/140‑1 (MQ=255)                                                        atatGGGATGGGAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGcac                                                                               <  2:103226/140‑1 (MQ=255)                                                          atGTGATTGAAGCGTGAATAATAATGCCTAATGCAACAAAACTGATAATTAATATACTGCTTATCAATCACATTAAGCCGTGGCGAAACTTCATCATCGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAg                                                                             <  2:568730/140‑1 (MQ=255)                                                                      cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACGTTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                 <  2:521767/140‑1 (MQ=255)                                                                      cGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGtt                                                                 <  1:561728/140‑1 (MQ=255)                                                                       gTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAATCTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                <  1:357540/140‑1 (MQ=255)                                                                       gTGAATAATAATGCCTAATGTAACAAAACTGATAATTAAGATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTtg                                                                <  2:197295/140‑1 (MQ=255)                                                                            taataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGct                                                           >  2:712960/1‑140 (MQ=255)                                                                               taatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTCCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGcttct                                                        >  2:327976/1‑140 (MQ=255)                                                                                              cAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                         <  1:265234/140‑1 (MQ=255)                                                                                              cAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                         <  1:118011/140‑1 (MQ=255)                                                                                                aaaCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAAt                                       <  1:132339/140‑1 (MQ=255)                                                                                                         attaatATAATGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCtt                              >  2:468210/1‑140 (MQ=255)                                                                                                          ttaatATACTTCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATATGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTa                             <  1:717231/140‑1 (MQ=255)                                                                                                            aatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaaa                           <  1:205761/140‑1 (MQ=255)                                                                                                                   tGCTTATCAATAACATTAAGCCGTGGTGAAATGTCATTAGTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGa                    <  2:396752/140‑1 (MQ=255)                                                                                                                      ttATCAATAACATTAAGCCGTGGTGAAAATTCATCATTGTTCTTTAGGTCTTTCAAATTTATAGCCTACGCCACGCACAGATTTAATAAGTTCTGGCTTCTTAGGATTATCTTCTACTTTATCTCTTAAATACCTCatat                 >  2:437468/1‑140 (MQ=255)                                                                                                                       tATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg                <  1:224054/140‑1 (MQ=255)                                                                                                                        aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGGTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGt               <  1:640071/140‑1 (MQ=255)                                                                                                                              aaCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTATGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATca         <  2:713394/140‑1 (MQ=255)                                                                                                                                     aGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  <  1:455693/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                         AAATATATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797637‑1797908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑