Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,426,675	G→A	10.9%	P88S (CCG→TCG)	PP_2127 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,426,675	0	G	A	10.9%	117.5 / 5.7	46	P88S (CCG→TCG)	PP_2127	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (18/23);  new base A (3/2);  total (21/25)
Fisher's exact test for biased strand distribution p-value = 6.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

AACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGCCC  >  NC_002947/2426530‑2426822                                                                                                                                                   |                                                                                                                                                     aaCTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGgcg‑c                                                                                                                                                 >  2:685004/1‑150 (MQ=255)   cTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCG‑Cat                                                                                                                                               <  2:883870/150‑2 (MQ=255)      gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCGGGCGCTCGACTTCTTGCGCCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTg                                                                                                                                            <  2:200700/150‑1 (MQ=255)         gggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGAt                                                                                                                                         >  1:287682/1‑150 (MQ=255)         gggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGAt                                                                                                                                         <  1:888036/150‑1 (MQ=255)          ggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATc                                                                                                                                        <  2:259779/150‑1 (MQ=255)                 gcCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGTCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTgg                                                                                                                                 >  1:1335897/1‑150 (MQ=255)                         aGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCgcccagg                                                                                                                         <  2:261717/150‑1 (MQ=255)                             aCTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCgcccaggccca                                                                                                                     >  2:185119/1‑150 (MQ=255)                               tGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCTGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGt                                                                                                                   <  1:1176998/150‑1 (MQ=255)                                gCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGtt                                                                                                                  <  2:287682/150‑1 (MQ=255)                                      gCAGCTTGGCAGCGGTGAGCAGTTGCCCGATGTCGTCGTGCAGTTCTCGGCCCAGATGCTGGCGCTCGTCTTCTTGCAGCTTTCGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CGGGTGGATCGTCGTGTGTCGCAGTCCCAGTTGtccga                                                                                                            >  2:85156/1‑146 (MQ=255)                                      gCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGAc                                                                                                                                     <  2:486889/125‑1 (MQ=255)                                      gCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGAc                                                                                                                                     >  1:486889/1‑125 (MQ=255)                                              gCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCACGTCTTCTTGCACCTTTAGCTTGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCAccc                                                                                                    >  1:530775/1‑150 (MQ=255)                                                       aGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CCCAAGGTTGGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCg                                                                                           >  1:448157/1‑150 (MQ=255)                                                           gTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCa                                                                                       >  1:411542/1‑150 (MQ=255)                                                              gACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACt                                                                                    <  1:685004/150‑1 (MQ=255)                                                                 cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCG‑Catg                                                                                                                                              <  1:1170680/89‑3 (MQ=37)                                                                 cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCG‑Catg                                                                                                                                              >  2:1170680/1‑87 (MQ=25)                                                                 cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTAGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTgca                                                                                 >  2:593518/1‑150 (MQ=255)                                                                   aTGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTgcagc                                                                               >  1:515026/1‑150 (MQ=255)                                                                     gtcgtcGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCAc                                                                             <  1:475058/150‑1 (MQ=255)                                                                            tGCAGTTCCCGGCCCAGAGGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGGGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAgg                                                                      >  2:57331/1‑150 (MQ=255)                                                                                        cccAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGAtt                                                          <  2:411542/150‑1 (MQ=255)                                                                                        cccAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACAAGCAGGCTGGCCGGGAtt                                                          <  1:825783/150‑1 (MQ=255)                                                                                                cTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGtt                                                  <  1:185119/150‑1 (MQ=255)                                                                                                     gcTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCgcccaggccca                                                                                                                     >  2:273918/1‑78 (MQ=255)                                                                                                     gcTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCgcccaggccca                                                                                                                     <  1:273918/78‑1 (MQ=255)                                                                                                         gTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAg                                            <  1:791097/147‑1 (MQ=255)                                                                                                         gTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGACCAg                                            >  2:791097/1‑147 (MQ=255)                                                                                                               ttGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTAGGCCAGGTACAgcgc                                   >  2:989954/1‑150 (MQ=255)                                                                                                                  cACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCAt                                <  2:159480/150‑1 (MQ=255)                                                                                                                     cTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGtt                             >  1:1176382/1‑150 (MQ=255)                                                                                                                     cTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGtt                             >  1:1141829/1‑150 (MQ=255)                                                                                                                       tGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTgg                           <  1:593518/150‑1 (MQ=255)                                                                                                                            ctGCGCCCGGCCGAGCT‑GGCCGAGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATc                      >  1:250276/2‑150 (MQ=255)                                                                                                                             tGCGCCCGGCCGAGCT‑GGCCGAGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCa                     >  1:508879/1‑150 (MQ=255)                                                                                                                                ccTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTg                  <  1:85156/149‑1 (MQ=255)                                                                                                                                 cTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGCCCAACTGCAGCACCAGCAGGCTGGCCGGGAGTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGa                 <  2:162759/150‑1 (MQ=255)                                                                                                                                 cTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGa                 <  2:1335897/150‑1 (MQ=255)                                                                                                                                    ggCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTgg                                                <  1:687352/116‑1 (MQ=255)                                                                                                                                    ggCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTgg                                                >  2:687352/1‑116 (MQ=255)                                                                                                                                             cGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGcaca      <  2:530775/150‑1 (MQ=255)                                                                                                                                                ctgggCGCCAGGTCGATCCACCT‑GCGCCC‑GGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGa                                                            >  2:482993/3‑92 (MQ=25)                                                                                                                                                ctgggCGCCAGGTCGATCCACCT‑GCGCCC‑GGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGa                                                            <  1:482993/90‑1 (MQ=25)                                                                                                                                                ccGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGcc   <  2:1141829/150‑1 (MQ=255)                                                                                                                                                 cGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGccc  <  2:515026/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     AACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCG‑CAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGAGGCCACGCACAGCCC  >  NC_002947/2426530‑2426822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑