Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,089,215	T→C	8.3%	A79A (GCA→GCG)	aroH ←	3‑deoxy‑7‑phosphoheptulonate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,089,215	0	T	C	8.3%	132.3 / 2.6	48	A79A (GCA→GCG)	aroH	3‑deoxy‑7‑phosphoheptulonate synthase
Reads supporting (aligned to +/- strand):  ref base T (24/20);  new base C (2/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.66e-01

GCCGATGGTTTCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTGGCCAGGGTCTGTTC  >  NC_002947/2089077‑2089361                                                                                                                                           |                                                                                                                                                              gCCGATGGTTTCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCg‑‑‑‑‑ag                                                                                                                                                 >  4:109589/1‑148 (MQ=255) gCCGATGGTTTCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCg‑‑‑‑‑ag                                                                                                                                                 >  4:68543/1‑148 (MQ=255)    gATGGTTTCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATCCGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAAAGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGTA‑‑‑‑‑Ct                                                                                                                                        >  5:306896/1‑149 (MQ=255)      tGGTTTCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑g                                                                                                                                     <  2:166879/149‑1 (MQ=255)         tttCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACTCCCCACTTTGACCACCGGGCAGCCGGCGGCAAATGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCg                                                                                                                                  <  5:219991/149‑1 (MQ=255)             aTCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCg‑‑‑‑‑a                                                                                                                                                  >  6:211011/1‑135 (MQ=255)             aTCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCg‑‑‑‑‑a                                                                                                                                                  <  5:211011/135‑1 (MQ=255)              tCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCAG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGct                                                                                                                             >  2:98455/1‑149 (MQ=255)              tCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCACGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGct                                                                                                                             >  5:223629/1‑149 (MQ=255)                 ccAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGTCAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCtctc                                                                                                                          >  5:30059/1‑149 (MQ=255)                                 tGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGccc                                                                                                          >  4:279434/1‑149 (MQ=255)                                     gAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGaa                                                                                                      <  3:109589/149‑1 (MQ=255)                                     gAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGaa                                                                                                      <  3:68543/149‑1 (MQ=255)                                     gAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGaa                                                                                                      <  1:121307/149‑1 (MQ=255)                                            ccGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGaaa                                                                                               <  3:279434/149‑1 (MQ=255)                                             cGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAg                                                                                              >  1:291876/1‑149 (MQ=255)                                             cGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAg                                                                                              >  7:192486/1‑149 (MQ=255)                                                  aTACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACg                                                                                         >  6:150367/1‑149 (MQ=255)                                                      gCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTCGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCt                                                                                     >  2:134623/1‑149 (MQ=255)                                                         ccACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCg                                                                                  >  1:308040/1‑149 (MQ=255)                                                          cACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCgg                                                                                 <  7:12291/149‑1 (MQ=255)                                                                caccacCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCt                                                                           >  7:31734/1‑149 (MQ=255)                                                                   caccGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCgg                                                                        <  2:291876/149‑1 (MQ=255)                                                                             ccGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCAc                                                                                          <  4:86584/121‑1 (MQ=255)                                                                             ccGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCAc                                                                                          >  3:86584/1‑121 (MQ=255)                                                                             ccGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTCGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCg                                                              <  1:134623/149‑1 (MQ=255)                                                                                          tCATGTCAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTcgcgc                                                 <  6:30059/149‑1 (MQ=255)                                                                                            aTGATAATGTACATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCAGCTCTCTCAACCCCCCTCAGGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGgcg                                                           <  1:98455/148‑1 (MQ=255)                                                                                            aTGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCgcgcgc                                               >  3:205125/1‑149 (MQ=255)                                                                                            aTGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCgcgcgc                                               >  1:74872/1‑149 (MQ=255)                                                                                            aTGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCgcgcgc                                               >  6:31131/1‑149 (MQ=255)                                                                                                       cATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGGCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCcgcg                                     >  3:56815/1‑148 (MQ=255)                                                                                                       cATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCcgcg                                     >  2:232337/1‑148 (MQ=255)                                                                                                         tttGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCTCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGaa                                   >  3:239131/1‑148 (MQ=255)                                                                                                              agcaACACCTTGAAGGTGTCGCGGATTTTCGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCg                                                                         <  4:231887/105‑1 (MQ=255)                                                                                                              agcaACACCTTGAAGGTGTCGCGGATTTTCGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCg                                                                         >  3:231887/1‑105 (MQ=255)                                                                                                               gcaACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAgc                            <  5:150367/149‑1 (MQ=255)                                                                                                                 aaCACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAgcgg                          <  2:308040/149‑1 (MQ=255)                                                                                                                  acacCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAgcggc                         >  3:167453/1‑149 (MQ=255)                                                                                                                      cTTGAAGGCGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGt                     <  2:182097/149‑1 (MQ=255)                                                                                                                        tGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAg                   >  6:157846/1‑149 (MQ=255)                                                                                                                            ggTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCTGGTAGCTgg               <  4:167453/149‑1 (MQ=255)                                                                                                                                tCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCCATAACCGCCCTGAAGCAGAAAGGAACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGACCACCAGCGGCGGGTAGCTGGCCAg           >  5:116764/1‑149 (MQ=255)                                                                                                                                tCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTgg               <  7:87084/145‑1 (MQ=255)                                                                                                                                tCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTgg               >  8:87084/1‑145 (MQ=255)                                                                                                                                   cgGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGGCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTGGCCAGGGt        <  4:56815/149‑1 (MQ=255)                                                                                                                                   cgGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTGGCCAGGGt        <  6:223629/149‑1 (MQ=255)                                                                                                                                   cgGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTGGCCAGGGt        <  1:232337/149‑1 (MQ=255)                                                                                                                                          ttGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTGGCCAGGGTCTGTTc  <  8:31734/148‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                              GCCGATGGTTTCATCGCCAGATGAGCGCGGTTTGGCGAACTGACCGGCCATACGCCCCACTTTCACCACCGGGCAGCCGGCGGCAAAGGTCATGACAATGGCCATTTGCAGCAACACCTTGAAGGTGTCGCGGATTTTTGCAGCCG‑‑‑‑‑AGAA‑‑‑‑‑CTC‑GGCGAAGCTCTCGGCGCAATCACCGCCCTGAAGCAGAAAGGCACGGCCTTCGGTGACCTCGGCGAACTGCCGGCGCAGCTCGCGCGCCTCACCCGCGAACACCAGCGGCGGGTAGCTGGCCAGGGTCTGTTC  >  NC_002947/2089077‑2089361

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: ‑