Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,801,450	T→C	11.7%	I47M (ATA→ATG)	aroK ←	shikimate kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,801,450	0	T	C	11.7%	127.6 / 7.7	51	I47M (ATA→ATG)	aroK	shikimate kinase
Reads supporting (aligned to +/- strand):  ref base T (23/22);  new base C (3/3);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

CCCGGCCACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAAT  >  NC_002947/5801302‑5801595                                                                                                                                                     |                                                                                                                                                  cccGGCCACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAat                                                                                                                                                   <  6:205628/149‑1 (MQ=255)       cACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAc                                                                                                                                             <  7:5490/149‑1 (MQ=255)        aCCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACg                                                                                                                                            <  7:281720/149‑1 (MQ=255)         cccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAc                                                                                                                                             >  3:95790/1‑147 (MQ=255)         cccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCAc                                                                                                                                             <  4:95790/147‑1 (MQ=255)         cccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACgg                                                                                                                                           <  3:169385/149‑1 (MQ=255)          ccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCCCCACACCGTCGAGCGCGCACAACTCGGCAATCAGAGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACggg                                                                                                                                          >  8:79061/1‑149 (MQ=255)          ccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACgg                                                                                                                                           >  4:37189/1‑148 (MQ=255)          ccTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATcccgtg                                                                                                                                           >  5:87995/1‑144 (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                                                                                                                                 >  7:99066/1‑132 (MQ=255)                                  cTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcgac                                                                                                                                 <  8:99066/134‑3 (MQ=255)                                             aCCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGt                                                                                                        <  3:287167/148‑1 (MQ=255)                                               cgcgCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCg                                                                                                      >  5:54859/1‑148 (MQ=255)                                               cgcgCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcga                                                                                                                                  >  4:189556/1‑119 (MQ=255)                                               cgcgCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAACATCCCGTGGATATTcga                                                                                                                                  <  3:189556/120‑2 (MQ=255)                                                    cACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                <  3:37189/149‑1 (MQ=255)                                                    cACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                >  5:85997/1‑149 (MQ=255)                                                    cACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATcc                                                                                                >  6:53647/1‑149 (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)                                                                     accacACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAata                                                                                                                                                  >  6:225439/1‑82 (MQ=255)                                                                     accacACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAata                                                                                                                                                  <  5:225439/82‑1 (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        <  1:179097/149‑1 (MQ=255)                                                                                                                                            cttGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGca        <  5:53647/149‑1 (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)                                                                                                                                                     |                                                                                                                                                  CCCGGCCACCCTGATGCAGCGCCTGCCGGTTGGCTTCGCGCATCACCGCGCCACCGCCGGTGGCCAGCACCACACCGTCGAGCGCGCACAACTCGGCAATCATCGCTTGCTCGCGATCACGGAAACCCGGCTCGCCTTCCTTGTCGAATATCCACGGGATGTTCGCGCCGCATCGCAGTTCGATTTCCTTGTCGGAATCCTTGAACAGCAGGCGCAGCTCTTTGGCCAACAGGCGTCCGATGGTGCTTTTACCAGCGCCCATGGGCCCCACAAGTATCAAATTTCGCACAGAAT  >  NC_002947/5801302‑5801595

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: ‑