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%	105.6 / NA	32	R7G (CGC→GGC)	phoR	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (15/17);  total (15/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797642‑1797908                                                                                                                                   |                                                                                                                                         tatGATCTTGTCTTGTTTGCTAGGGCTTGTTCGTTTTTTTCTGATAAAACATATGTGATTGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATACCATTAAGCCGTGGTGaacc                                                                                                                                <  2:185860/141‑3 (MQ=255)   tGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACtt                                                                                                                              >  2:216719/1‑141 (MQ=255)          gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                       <  1:54062/141‑1 (MQ=255)          gCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCAtt                                                                                                                       <  1:272301/141‑1 (MQ=255)                tttGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCtt                                                                                                                 <  1:19552/140‑1 (MQ=255)                    cTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAgg                                                                                                             >  1:49100/1‑141 (MQ=255)                               tCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTTTTCTTTCGGTCTTCCCCAtt                                                                                                  >  2:70853/1‑141 (MQ=255)                                cGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAAttt                                                                                                 >  2:81684/1‑141 (MQ=255)                                           gATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGc                                                                                      >  2:214709/1‑141 (MQ=255)                                                      tgtgATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTGATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGACCAGtt                                                                           >  2:59654/1‑141 (MQ=255)                                                            ggAAGCGTGAATAATAATGTCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaata                                                                     <  2:248664/141‑1 (MQ=255)                                                            ggAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTtaata                                                                     <  1:81684/141‑1 (MQ=255)                                                                    gAATAATAATGCCTGATGTAACAAAACTGGTAATTAAAATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATAGTTCTTTAGGTCTTTCCAACTTATAGCCTAAGCAACGCACAGTTTTAATAATTtgttg                                                             >  2:209132/1‑139 (MQ=255)                                                                     attaatattTCCTACTGTTACATAAATGATTATTCATATATCTCTTAGCAATAACATGAAGCCTGGGTGAAACTTTATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGc                                                            <  2:219090/139‑1 (MQ=255)                                                                     aataataatGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGc                                                            <  2:212333/141‑1 (MQ=255)                                                                            atGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAg                                                     >  2:186732/1‑141 (MQ=255)                                                                                  aaTGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAt                                               <  2:211553/141‑1 (MQ=255)                                                                                     gTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTAtctt                                            <  1:214709/141‑1 (MQ=255)                                                                                      tAACAAACCTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTATGGAGTTGTGGCCTCTTAGGATTAtcttc                                           <  2:257097/141‑1 (MQ=255)                                                                                        aCAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTa                                         >  2:240387/1‑141 (MQ=255)                                                                                                gATAATTAATATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTAtct                                 <  1:114741/141‑1 (MQ=255)                                                                                                     ttaatATACTGCTTATCAATAGCATTGTGACGTGGTGAAACTTCAGCATTGTTCTTTAGGTCTTTCATTTTTATAGCCTATGCCTCGCAGAGTTTTACTAAGTTGTGGCTTATTGGGTTTTTCATCTAATTTATCTATTaa                            >  2:155644/1‑141 (MQ=255)                                                                                                      taatATACTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTaaa                           <  1:223585/141‑1 (MQ=255)                                                                                                            aCTGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTg                     >  1:260420/1‑141 (MQ=255)                                                                                                              tGCTTATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGat                   <  1:210298/141‑1 (MQ=255)                                                                                                                 ttATCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATg                <  1:216719/141‑1 (MQ=255)                                                                                                                   aTCAATAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTa              >  2:205212/1‑141 (MQ=255)                                                                                                                      aaTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACAt           <  2:246414/141‑1 (MQ=255)                                                                                                                       aTAACATTAAGCCGTGGTGAACCTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc          <  2:120805/141‑1 (MQ=255)                                                                                                                       aTAACATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTACAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGAGTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATc          >  1:256017/1‑141 (MQ=255)                                                                                                                          aCATTAAGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGCCTGATATGTACATcaac       >  1:112129/1‑141 (MQ=255)                                                                                                                               aaGCCGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTc  >  1:32458/1‑141 (MQ=255)                                                                                                                                   |                                                                                                                                         TATGATCTTGCATCTGTTGCTAGAGCTTGTTCGTGTTTTTCTGATAAAACATATGTGATGGAAGCGTGAATAATAATGCCTAATGTAACAAAACTGATAATTAATATACTGCTTATCAATAACATTAAGCGGTGGTGAAACTTCATCATTGTTCTTTAGGTCTTTCCAATTTATAGCCTAAGCCACGCACAGTTTTAATAAGTTGTGGCTTCTTAGGATTATCTTCTAATTTATCTCTTAAATGACTGATATGTACATCAACAATTC  >  CP000730/1797642‑1797908

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑