Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,801,455	A→C	9.7%	W46G (TGG→GGG)	aroK ←	shikimate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,801,455	0	A	C	9.7%	135.7 / 7.4	52	W46G (TGG→GGG)	aroK	shikimate kinase
Reads supporting (aligned to +/- strand):  ref base A (25/21);  new base C (2/3);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.93e-01

CACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAATCAACGA  >  NC_002947/5801308‑5801601                                                                                                                                                    |                                                                                                                                                   cACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAc                                                                                                                                                   <  7:5490/149‑1 (MQ=255)  aCCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACg                                                                                                                                                  <  7:281720/149‑1 (MQ=255)   cccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAc                                                                                                                                                   <  4:95790/147‑1 (MQ=255)   cccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAc                                                                                                                                                   >  3:95790/1‑147 (MQ=255)   cccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACgg                                                                                                                                                 <  3:169385/149‑1 (MQ=255)    ccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCCCCACACCGTCGAGCGCGCACAACTCGGCAATCAGAGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACggg                                                                                                                                                >  8:79061/1‑149 (MQ=255)    ccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACgg                                                                                                                                                 >  4:37189/1‑148 (MQ=255)            aGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcga                                                                                                                                        <  6:87995/149‑2 (MQ=255)             gcgcCTGCCGGTTGGCTTCGCGCATCACCGCCCCACCGCCGGTGGCCAGCACCACACCCTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCATACTTGTCGAATATCCACGGGATGATcgcg                                                                                                                                       >  4:99284/1‑149 (MQ=255)                 cTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACgg                                                                                                                                                 >  1:304347/1‑135 (MQ=255)                 cTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACgg                                                                                                                                                 <  2:304347/135‑1 (MQ=255)                        ttGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAAGGGATGTTAGCGCCGCATCGCAg                                                                                                                            >  7:105976/1‑149 (MQ=255)                            cTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTc                                                                                                                         >  1:283849/1‑148 (MQ=255)                            cTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcgac                                                                                                                                       <  8:99066/134‑3 (MQ=255)                            cTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcgac                                                                                                                                       >  7:99066/1‑132 (MQ=255)                                       aCCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGt                                                                                                              <  3:287167/148‑1 (MQ=255)                                         cgcgCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCg                                                                                                            >  5:54859/1‑148 (MQ=255)                                         cgcgCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcga                                                                                                                                        <  3:189556/120‑2 (MQ=255)                                         cgcgCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcga                                                                                                                                        >  4:189556/1‑119 (MQ=255)                                              cACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                      >  5:85997/1‑149 (MQ=255)                                              cACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                      >  6:53647/1‑149 (MQ=255)                                              cACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                      <  3:37189/149‑1 (MQ=255)                                               aCCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCt                                                                                                     >  7:202474/1‑149 (MQ=255)                                                ccgccgGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCtt                                                                                                    <  4:277127/149‑1 (MQ=255)                                                ccgccgGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCtt                                                                                                    <  6:85997/149‑1 (MQ=255)                                                    cgGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                      <  5:37475/143‑1 (MQ=255)                                                    cgGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGAATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                      >  6:37475/1‑143 (MQ=255)                                                       tGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGAtt                                                                                                                     <  6:258619/125‑1 (MQ=255)                                                       tGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGCCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGAtt                                                                                                                     >  5:258619/1‑125 (MQ=255)                                                          ccAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAgg                                                                                          <  8:175460/149‑1 (MQ=255)                                                          ccAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAgg                                                                                          <  6:54859/149‑1 (MQ=255)                                                           cAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGgc                                                                                         >  4:198997/1‑149 (MQ=255)                                                                   caacGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCGCGCCTTCCTTGTCGAATATCCTCGGGATGTTCGCTCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGctct                                                                                 <  1:86133/146‑1 (MQ=255)                                                                    acCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCtt                                                                                >  5:181071/1‑149 (MQ=255)                                                                     ccGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCttt                                                                               <  6:181071/149‑1 (MQ=255)                                                                                gcACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGc                                                                    <  2:283849/149‑1 (MQ=255)                                                                                         ggCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTAGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACATCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATgg                                                           >  2:218185/1‑149 (MQ=255)                                                                                                         tCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGcc                                           >  3:156614/1‑149 (MQ=255)                                                                                                             gATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATg                                       >  7:23975/1‑149 (MQ=255)                                                                                                                  cGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGccc                                  <  7:79061/149‑1 (MQ=255)                                                                                                                         ccGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAg                            >  2:179097/1‑148 (MQ=255)                                                                                                                                gcattccttGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCaaa                     <  1:218185/145‑1 (MQ=255)                                                                                                                                gCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCaaa                     <  4:156614/148‑1 (MQ=255)                                                                                                                                  cttccttGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAAttt                  >  2:105513/1‑149 (MQ=255)                                                                                                                                      cttGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGca              <  5:53647/149‑1 (MQ=255)                                                                                                                                      cttGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGca              <  1:179097/149‑1 (MQ=255)                                                                                                                                         gTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGca              >  7:58717/1‑146 (MQ=255)                                                                                                                                            gAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTc                 >  2:275981/1‑140 (MQ=255)                                                                                                                                            gAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTc                 <  1:275981/140‑1 (MQ=255)                                                                                                                                            gAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAAt        >  1:238828/1‑149 (MQ=255)                                                                                                                                                  ccACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAATCAACGa  >  1:148592/1‑149 (MQ=255)                                                                                                                                                  ccACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAATCAACGa  >  4:213882/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                   CACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAATCAACGA  >  NC_002947/5801308‑5801601

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑