Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,426,664:1	+G	11.6%	coding (273/942 nt)	PP_2127 ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,426,664	1	.	G	11.6%	147.3 / 15.9	43	coding (273/942 nt)	PP_2127	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base . (18/20);  new base G (3/2);  total (21/22)
Fisher's exact test for biased strand distribution p-value = 6.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.09e-01

AACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGA  >  NC_002947/2426530‑2426807                                                                                                                                        |                                                                                                                                                aaCTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGgcgc                                                                                                                                  >  2:685004/1‑150 (MQ=255)   cTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCGCat                                                                                                                                <  2:883870/150‑2 (MQ=255)      gtcgGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCGGGCGCTCGACTTCTTGCGCCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTg                                                                                                                             <  2:200700/150‑1 (MQ=255)         gggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGAt                                                                                                                          <  1:888036/150‑1 (MQ=255)         gggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGAt                                                                                                                          >  1:287682/1‑150 (MQ=255)          ggCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATc                                                                                                                         <  2:259779/150‑1 (MQ=255)                 gcCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGTCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTgg                                                                                                                  >  1:1335897/1‑150 (MQ=255)                         aGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCgcccagg                                                                                                          <  2:261717/150‑1 (MQ=255)                             aCTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCgcccaggccca                                                                                                      >  2:185119/1‑150 (MQ=255)                               tGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCTGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGt                                                                                                    <  1:1176998/150‑1 (MQ=255)                                gCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGtt                                                                                                   <  2:287682/150‑1 (MQ=255)                                      gCAGCTTGGCAGCGGTGAGCAGTTGCCCGATGTCGTCGTGCAGTTCTCGGCCCAGATGCTGGCGCTCGTCTTCTTGCAGCTTTCGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCGGGTGGATCGTCGTGTGTCGCAGTCCCAGTTGtccga                                                                                             >  2:85156/1‑146 (MQ=255)                                      gCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGAc                                                                                                                      >  1:486889/1‑125 (MQ=255)                                      gCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGAc                                                                                                                      <  2:486889/125‑1 (MQ=255)                                              gCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCACGTCTTCTTGCACCTTTAGCTTGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCAccc                                                                                     >  1:530775/1‑150 (MQ=255)                                                       aGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCCCAAGGTTGGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCg                                                                            >  1:448157/1‑150 (MQ=255)                                                           gTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCa                                                                        >  1:411542/1‑150 (MQ=255)                                                              gACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACt                                                                     <  1:685004/150‑1 (MQ=255)                                                                 cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCGCatg                                                                                                                               >  2:1170680/1‑87 (MQ=25)                                                                 cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCCCGGCCGAGCT‑GGCCGAGCGCatg                                                                                                                               <  1:1170680/89‑3 (MQ=37)                                                                 cGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTAGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTgca                                                                  >  2:593518/1‑150 (MQ=255)                                                                   aTGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTgcagc                                                                >  1:515026/1‑150 (MQ=255)                                                                     gtcgtcGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCAc                                                              <  1:475058/150‑1 (MQ=255)                                                                            tGCAGTTCCCGGCCCAGAGGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGGGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAgg                                                       >  2:57331/1‑150 (MQ=255)                                                                                        cccAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGAtt                                           <  2:411542/150‑1 (MQ=255)                                                                                        cccAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACAAGCAGGCTGGCCGGGAtt                                           <  1:825783/150‑1 (MQ=255)                                                                                                cTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGtt                                   <  1:185119/150‑1 (MQ=255)                                                                                                     gcTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCgcccaggccca                                                                                                      <  1:273918/78‑1 (MQ=255)                                                                                                     gcTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCgcccaggccca                                                                                                      >  2:273918/1‑78 (MQ=255)                                                                                                         gTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAg                             <  1:791097/147‑1 (MQ=255)                                                                                                         gTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGACCAg                             >  2:791097/1‑147 (MQ=255)                                                                                                               ttGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTAGGCCAGGTACAgcgc                    >  2:989954/1‑150 (MQ=255)                                                                                                                  cACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCAt                 <  2:159480/150‑1 (MQ=255)                                                                                                                     cTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGtt              >  1:1176382/1‑150 (MQ=255)                                                                                                                     cTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGtt              >  1:1141829/1‑150 (MQ=255)                                                                                                                       tGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTgg            <  1:593518/150‑1 (MQ=255)                                                                                                                            ctGCGCCCGGCCGAGCT‑GGCCGAGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATc       >  1:250276/2‑150 (MQ=255)                                                                                                                             tGCGCCCGGCCGAGCT‑GGCCGAGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCa      >  1:508879/1‑150 (MQ=255)                                                                                                                                ccTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTg   <  1:85156/149‑1 (MQ=255)                                                                                                                                 cTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGCCCAACTGCAGCACCAGCAGGCTGGCCGGGAGTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGa  <  2:162759/150‑1 (MQ=255)                                                                                                                                 cTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGa  <  2:1335897/150‑1 (MQ=255)                                                                                                                                    ggCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTgg                                 <  1:687352/116‑1 (MQ=255)                                                                                                                                    ggCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTgg                                 >  2:687352/1‑116 (MQ=255)                                                                                                                                        |                                                                                                                                                AACTCGTCGGGCATGCGCCGTTGCAGCCACTGCAGTTGCAGCTTGGCAGCGGTGAGCAGTTGACCGATGTCGTCGTGCAGTTCCCGGCCCAGATGCTGGCGCTCGTCTTCTTGCACCTTGAGCATGCGCTCGGCC‑AGCTCGGCCGGGCGCAGGTGGATCGACCTGGCGCCCAGGCCCAGTTGTACAACAGCACCCAGCGTGGCGACCAACTGCAGCACCAGCAGGCTGGCCGGGATTGCCTGGTTGGCCAGGTACAGCGCCATGTTGGCAATCAGTGA  >  NC_002947/2426530‑2426807

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: ‑