Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,797,152	G→A	17.8%	S213S (TCC→TCT)	phoR ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,797,152	0	G	A	17.8%	86.0 / 11.0	38	S213S (TCC→TCT)	phoR	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (16/15);  new base A (3/4);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.91e-01

CCGTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAATTGTGTTGC  >  CP000730/1797012‑1797292                                                                                                                                             |                                                                                                                                             ccGTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTg                                                                                                                                              >  2:419730/1‑141 (MQ=255)   gTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGa                                                                                                                                            >  1:84936/1‑141 (MQ=255)       tAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGa                                                                                                                                        <  1:172717/141‑1 (MQ=255)       tAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGa                                                                                                                                        <  1:172719/141‑1 (MQ=255)        aGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGaa                                                                                                                                       >  1:296875/1‑141 (MQ=255)          ccTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAAtt                                                                                                                                     >  2:262366/1‑141 (MQ=255)          ccTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAAtt                                                                                                                                     >  2:447611/1‑141 (MQ=255)          ccTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAAtt                                                                                                                                     >  2:255119/1‑141 (MQ=255)           cTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTCGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAAttt                                                                                                                                    >  2:389839/1‑141 (MQ=255)                                     ttGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAgg                                                                                                          >  1:183139/1‑141 (MQ=255)                                       gAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGcg                                                                                                        >  1:386282/1‑141 (MQ=255)                                        aaCTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGcgt                                                                                                       >  1:242528/1‑141 (MQ=255)                                          cTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGcgtcg                                                                                                     <  1:139953/141‑1 (MQ=255)                                          cTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTATTGCTCATTATTAAGCTTTTGAAGGcgtcg                                                                                                     <  2:413484/141‑1 (MQ=255)                                            gTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTg                                                                                                   <  1:151851/141‑1 (MQ=255)                                            gTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTg                                                                                                   <  1:315812/141‑1 (MQ=255)                                            gTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTCTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTg                                                                                                   <  1:233221/141‑1 (MQ=255)                                                      cGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCAtt                                                                                         >  1:443771/1‑141 (MQ=255)                                                             tttGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGac                                                                                  >  1:303596/1‑141 (MQ=255)                                                             tttGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGac                                                                                  >  1:53378/1‑141 (MQ=255)                                                                 caacaaCGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGTCTCaa                                                                              >  2:362870/1‑141 (MQ=255)                                                                 caacaaCGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACaa                                                                              >  1:309934/1‑141 (MQ=255)                                                                         aTTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCt                                                                      >  1:380872/1‑141 (MQ=255)                                                                         aTTTTTCCATTTCGATCTATCATTAAAATAGCACTCGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGCGCTAAATCATTGGTAGACACAAAAAACGCt                                                                      >  1:329903/1‑141 (MQ=255)                                                                          tttttCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCtt                                                                     <  1:154278/141‑1 (MQ=255)                                                                                    tcgataaaaaaTTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCAAAAAAAAAAAAAAAAAGCGCTTTAGTTTCTac                                                           <  2:155761/131‑1 (MQ=255)                                                                                    tCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTac                                                           <  2:36558/141‑1 (MQ=255)                                                                                    tCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGAAACAAAAAGCGCTTTAGTTTCTac                                                           <  2:155816/141‑1 (MQ=255)                                                                                             cATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACt                                                  <  2:443771/141‑1 (MQ=255)                                                                                                  aaaTAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAg                                             <  1:262366/141‑1 (MQ=255)                                                                                                  aaaTAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAg                                             <  1:255119/141‑1 (MQ=255)                                                                                                  aaaTAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTAGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAg                                             <  1:447611/141‑1 (MQ=255)                                                                                                               aaTATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTAtgtg                                >  1:187617/1‑141 (MQ=255)                                                                                                                atatTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGa                               >  1:26428/1‑141 (MQ=255)                                                                                                                atatTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGa                               >  2:336230/1‑141 (MQ=255)                                                                                                                             ttgttTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTg                  <  2:380872/141‑1 (MQ=255)                                                                                                                             ttgttATTAAACGGTTAGATTTAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACTCGTATGTGATAATAACCATTTg                  <  2:329903/141‑1 (MQ=255)                                                                                                                                     aaaCGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATAAGTAAACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAAt          <  2:296875/141‑1 (MQ=255)                                                                                                                                      aaCGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAAtt         <  1:455110/141‑1 (MQ=255)                                                                                                                                             ggATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAATTGTGTTGc  <  1:176271/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                             CCGTGATAGCCTACTTGTTCAATATTATGCGAGATGTTGAACTGTTCATAATACGCTTTATTTGCAACAACGATTTTTCCATTTCGATCTATCATTAAAATAGCACTTGGAATATTTTCAATCGTTGTTTTTAAACGGTTGGATTGAATTTTTTGCTCATTATTAAGCTTTTGAAGGCGTCGTGCTAAATCATTGGTAGACACAAAAAGCGCTTTAGTTTCTACAACATTACTTTCAGGTACACGTATGTGATAATAACCATTTGCCAACAATTGTGTTGC  >  CP000730/1797012‑1797292

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