Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,544,627	G→T	11.5%	A492A (GCC→GCA)	ampG ←	muropeptide permease AmpG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,544,627	0	G	T	11.5%	144.0 / 9.6	52	A492A (GCC→GCA)	ampG	muropeptide permease AmpG
Reads supporting (aligned to +/- strand):  ref base G (25/21);  new base T (3/3);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.66e-01

GCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCGGCAACAGCAGCATGATCGAACTGAGCAGCGCGTACTGG  >  NC_002947/1544480‑1544771                                                                                                                                                    |                                                                                                                                                  gCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAggg                                                                                                                                                  <  1:210607/149‑1 (MQ=255)     cTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgat                                                                                                                                              >  3:27484/1‑149 (MQ=37)        cacaGGGCCCCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGCTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatcag                                                                                                                                           >  2:179031/1‑149 (MQ=255)         acaGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATCGCCCTGCAGTGGcatcag                                                                                                                                           <  8:268347/148‑1 (MQ=38)         acaGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATCGCCCTGCAGTGGcatcag                                                                                                                                           >  7:268347/1‑148 (MQ=38)         acaGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATCGCCCTGCAGTGGcatcag                                                                                                                                           >  4:233227/1‑148 (MQ=38)           aGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatcaggat                                                                                                                                        <  6:85590/149‑1 (MQ=255)           aGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATCGCCCTGCAGTGGcatcaggaa                                                                                                                                        <  3:233227/149‑2 (MQ=38)            gggCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatcaggat                                                                                                                                        >  4:228710/1‑148 (MQ=255)               ccgcgccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATCGCCCTGCAGTGGcatcaggaagccg                                                                                                                                    >  1:141427/1‑144 (MQ=38)               ccgcgccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATCGCCCTGCAGTGGcatcaggaagccg                                                                                                                                    <  2:141427/149‑6 (MQ=38)                     cgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGc                                                                                                                             >  2:260303/1‑149 (MQ=255)                           gTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCAccccc                                                                                                                       >  7:40470/1‑149 (MQ=255)                                    ggTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGcc                                                                                                              >  2:100412/1‑149 (MQ=255)                                           ccGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGAt                                                                                                         >  4:300636/1‑147 (MQ=255)                                             gcgAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAgg                                                                                                     <  3:140681/149‑1 (MQ=255)                                             gcgAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAg                                                                                                      >  1:69597/1‑148 (MQ=255)                                             gcgAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCCCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAg                                                                                                      >  8:271829/1‑148 (MQ=255)                                               gAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGgaa                                                                                                   <  1:179031/149‑1 (MQ=255)                                                aaGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAgg                                                                                                     >  5:120979/1‑146 (MQ=255)                                                   agGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGaagaag                                                                                               <  3:228710/149‑1 (MQ=255)                                                        aGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTg                                                                                          >  8:48671/1‑149 (MQ=255)                                                        aGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTg                                                                                          <  7:48671/149‑1 (MQ=255)                                                         gCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTgg                                                                                         <  7:271829/149‑1 (MQ=255)                                                         gCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTgg                                                                                         <  1:260303/149‑1 (MQ=255)                                                          cacaGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGt                                                                                        <  4:27484/149‑1 (MQ=255)                                                           acaGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTgg                                                                                         >  6:118066/1‑147 (MQ=255)                                                               gCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTgg                                                                                         >  3:17280/1‑143 (MQ=255)                                                               gCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTgg                                                                                         <  4:17280/143‑1 (MQ=255)                                                                  aTACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAAc                                                                                <  8:40470/149‑1 (MQ=255)                                                                   tACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACt                                                                               >  1:16396/1‑149 (MQ=255)                                                                      aaaGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAg                                                                                      >  5:186531/1‑139 (MQ=255)                                                                      aaaGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAg                                                                                      <  6:186531/139‑1 (MQ=255)                                                                         gCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTTCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGTAAGAAGTCGTGGTAGCCGAACTTCTCca                                                                         <  5:118066/149‑1 (MQ=255)                                                                         gCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCca                                                                         <  2:16396/149‑1 (MQ=255)                                                                              aGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCCGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACaa                                                                      <  1:100412/148‑1 (MQ=255)                                                                                ggCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGAGATCAGGATCAC‑CGTAGGCACCCCCAGCAGCGCCCTGATCATGAAGAAGTCGTGGTAGCAGAACTTCTCCACAATAAc                                                                  >  8:195919/1‑149 (MQ=255)                                                                                   cGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGcc                                                               <  6:120979/149‑1 (MQ=255)                                                                                           cACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATAcc                                                       <  3:300636/149‑1 (MQ=255)                                                                                            aCCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAg                                                                                      >  7:254961/1‑117 (MQ=255)                                                                                            aCCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAg                                                                                      <  8:254961/117‑1 (MQ=255)                                                                                                  tGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAAt                                                >  2:211305/1‑149 (MQ=255)                                                                                                    gtcgtcCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAAt                                                >  6:83114/1‑147 (MQ=255)                                                                                                          cGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCcgcg                                        >  6:282877/1‑149 (MQ=255)                                                                                                              aCCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCGGCaa                                    <  2:69597/149‑1 (MQ=255)                                                                                                                        cccgcccgGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGCACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCgg                                       >  6:332926/1‑136 (MQ=255)                                                                                                                         ccgcccgGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCGGCAACAGCAGCATGa                         >  2:283478/1‑149 (MQ=255)                                                                                                                          cgcccgGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTtct                                                                            >  6:334183/1‑97 (MQ=255)                                                                                                                          cgcccgGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTtct                                                                            <  5:334183/97‑1 (MQ=255)                                                                                                                              cgGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGGCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCAGAATAACGCGCGAATACCCGCCAATCAGCCGCGGCAACAGCAGCATGATCGaa                    <  7:195919/149‑1 (MQ=255)                                                                                                                                       gATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCGCAATAACGCGCGAATACCCGCCAATCAGCCGCGGCAACAGCAGCATGATCGAACTGagcagc           >  8:228045/1‑149 (MQ=255)                                                                                                                                          gCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCGGCAAcagca                               >  8:152138/1‑126 (MQ=255)                                                                                                                                                 cAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCGGCAACAGCAGCATGATCGAACTGAGCAGCGCGTACTgg  <  3:241780/148‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  GCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAG‑CGTAGGCACCCCCAGCAGCGCCGTGATCAGGAAGAAGTCGTGGTAGCCGAACTTCTCCACAATAACGCCCGAATACCCGCCAATCAGCCGCGGCAACAGCAGCATGATCGAACTGAGCAGCGCGTACTGG  >  NC_002947/1544480‑1544771

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑