Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	4,049,665	A→C	31.8%	I12S (ATC→AGC)	glnL ←	sensory histidine kinase in two‑component regulatory system with GlnG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	4,049,665	0	A	C	31.8%	23.0 / 20.8	32	I12S (ATC→AGC)	glnL	sensory histidine kinase in two‑component regulatory system with GlnG
Reads supporting (aligned to +/- strand):  ref base A (8/13);  new base C (5/5);  total (13/19)
Fisher's exact test for biased strand distribution p-value = 7.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.27e-01

AAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAATTGACGGAGAAAAAAGCCCATGCAGAGATGG  >  CP009273/4049524‑4049809                                                                                                                                              |                                                                                                                                                  aaGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGAt                                                                                                                                                  <  2:290521/143‑1 (MQ=255)          aaCAGTCCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTCGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTCATGGGTCGCCAGGTTGTCATCGATTAGCAAAATACTGTTAATCAGCGAGTTGTGGCTCTGCCCAGc                                                                                                                                         <  2:285972/143‑1 (MQ=255)                       aCGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGtt                                                                                                                      <  1:34846/149‑1 (MQ=255)                       aCGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGtt                                                                                                                      <  1:34844/149‑1 (MQ=255)                          gtgtACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCt                                                                                                                         >  2:438360/1‑143 (MQ=255)                               ccAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATaaa                                                                                                              <  1:517312/149‑1 (MQ=255)                                   aCAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATa                                                                                                                >  2:443038/1‑143 (MQ=255)                                      aTTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAg                                                                                                             <  2:468731/143‑1 (MQ=255)                                      aTTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCCGGCTGCGTGCCTGTTGCCATAAAg                                                                                                             >  2:195162/1‑143 (MQ=255)                                                 cTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGt                                                                                           <  1:239476/149‑1 (MQ=255)                                                   ttGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTg                                                                                         <  1:500377/149‑1 (MQ=255)                                                            cAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGGTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGACTGTTGCCATAAAGCAGTCCCCTG‑GACAGGGTGCACCAtttt                                                                                >  1:181685/1‑149 (MQ=255)                                                               ttgttgCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAGATGCTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGt                                                                             >  1:104332/1‑149 (MQ=255)                                                                     cgcgGCAGGGTAGGCGTATTGGGCCGCCAGGTTGCCATCGCTTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAGAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGt                                                                             <  2:455154/143‑1 (MQ=255)                                                                        ggCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAg                                                                    >  1:41205/1‑149 (MQ=255)                                                                             ggTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCtttt                                                               >  1:312490/1‑149 (MQ=255)                                                                                  gCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACgg                                                          >  1:77298/1‑149 (MQ=255)                                                                                  gCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACgg                                                          <  1:466400/149‑1 (MQ=255)                                                                                     tAATGGATCGCCAGGTGGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTa                                                             <  2:48002/143‑1 (MQ=255)                                                                                         ggATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGGGCCTTATAGCTTTTTACGGATaaaaa                                                   >  1:24498/1‑149 (MQ=255)                                                                                           atggCCAGGTTTCCATCGATGAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAgc                                                 <  1:456833/146‑1 (MQ=255)                                                                                            tCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCACTATAGCTTTTTACGGATAAAAAgcg                                                <  1:315392/149‑1 (MQ=255)                                                                                                     tGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTCTTTACGGATAAAAAGCGCGAAGCATc                                       >  1:83546/1‑149 (MQ=255)                                                                                                       tCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAg                                           <  2:340158/143‑1 (MQ=255)                                                                                                         aTCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCa                                         <  2:318099/143‑1 (MQ=255)                                                                                                             aTTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGCTAAAAAGCGCGAAGCATCag                                     >  2:130898/1‑143 (MQ=255)                                                                                                                         cTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAACCGCGCTGAGCATCagccactcggcgta                         <  2:217811/143‑13 (MQ=255)                                                                                                                                tCAGCGGGTTGAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAATTGACGGAGaaaaaa                  <  2:71879/143‑1 (MQ=255)                                                                                                                                gcAGCAAGTTGAGGTTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAATTGACGGAGaaaaaa                  <  2:238176/142‑1 (MQ=255)                                                                                                                                          gAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAATTGACGGAGAAAAAAGCCCATGCag        >  2:28014/1‑143 (MQ=255)                                                                                                                                          gAGGCTCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCCA‑ATTGGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAAGTGACGGAGAAAAAAGCCCATGCAGAGATgg  >  1:413207/1‑149 (MQ=255)                                                                                                                                             gATCCGCCCAGCAGCGGGGTGCGGGCCTGTTGCCATAAAGAAGTCCCCTGCAACA‑TTTGAACCGTTTGAGGGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAATTGACGGAGAAAAAAGCCCATGCAgaga     <  2:51533/143‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                  AAGTAGCTCAACAGTTCCGGTAACGGTGTACCAAACAATTTGCGGGAGCTTTGGGCGAGCAGTTGTTGCGCGGCAGGGTTGGCGTAATGGATCGCCAGGTTGTCATCGATTAACAAAATACTGTTAATCAGCGAGTTGAGGATCTGCCCAGCATCGGGCTGCGTGCCTGTTGCCATAAAGCAGTCTCCTG‑AACAGGTTGCACCATTTTAGTGCATTATAGCTTTTTACGGATAAAAAGCGCGAAGCATCAGAGAATTGACGGAGAAAAAAGCCCATGCAGAGATGG  >  CP009273/4049524‑4049809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑