Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	770,543	T→C	11.2%	V76A (GTC→GCC) ‡	PP_0662 →	threonine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	770,543	0	T	C	11.2%	135.5 / 7.3	53	V76A (GTC→GCC) ‡	PP_0662	threonine synthase
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base C (3/3);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTATGTGCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCTTTG  >  NC_002947/770402‑770683                                                                                                                                              |                                                                                                                                             tttATGTGCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGa                                                                                                                                        >  2:128222/1‑148 (MQ=255)    aTGTGCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAg                                                                                                                                     <  3:134076/148‑1 (MQ=255)     tgtgCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAg                                                                                                                                     <  4:54029/147‑1 (MQ=255)     tgtgCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAg                                                                                                                                     >  3:54029/1‑147 (MQ=255)      gtgCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTa                                                                                                                                  >  8:136466/1‑149 (MQ=255)         cccACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATcg                                                                                                                               >  6:65153/1‑149 (MQ=255)          ccACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATcgc                                                                                                                              <  5:282238/149‑1 (MQ=255)          ccACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATcgc                                                                                                                              >  7:234470/1‑149 (MQ=255)           cACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATcgcg                                                                                                                             >  4:10738/1‑149 (MQ=255)            aCCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACACTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCgg                                                                                                                            >  7:70334/1‑149 (MQ=255)              cTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGt                                                                                                                          <  1:128222/149‑1 (MQ=255)                 ggTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCCGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTcc                                                                                                                       <  3:245292/149‑1 (MQ=255)                        gtgtTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACcg                                                                                                                >  6:272704/1‑149 (MQ=255)                                 ccACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTgc                                                                                                       <  8:234470/149‑1 (MQ=255)                                   acaGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTgcgc                                                                                                     >  3:127446/1‑149 (MQ=255)                                   acaGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTgcgc                                                                                                     >  2:293883/1‑149 (MQ=255)                                   acaGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTgcgc                                                                                                     >  5:98466/1‑149 (MQ=255)                                   acaGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTgcgc                                                                                                     >  5:91584/1‑149 (MQ=255)                                   acaGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTgcgc                                                                                                     <  5:272704/149‑1 (MQ=255)                                      ggAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGt                                                                                                  <  2:100439/149‑1 (MQ=255)                                       gAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGtt                                                                                                 <  7:136466/149‑1 (MQ=255)                                          aTTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTgca                                                                                              <  6:98466/149‑1 (MQ=255)                                           ttGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTgcag                                                                                             <  3:10738/149‑1 (MQ=255)                                                     gTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGc                                                                                    >  7:241962/1‑148 (MQ=255)                                                       cGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCa                                                                                  >  3:176589/1‑148 (MQ=255)                                                                 cTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTg                                                                                      <  5:203484/134‑1 (MQ=255)                                                                 cTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTg                                                                                      >  6:203484/1‑134 (MQ=255)                                                                    cgacgaACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATc                                                                     <  5:65153/148‑1 (MQ=255)                                                                        gaACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAg                                                                                                                                           >  1:258349/1‑74 (MQ=255)                                                                        gaACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAg                                                                                                                                           <  2:258349/74‑1 (MQ=255)                                                                        gaACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTg                                                                  >  5:274846/1‑147 (MQ=255)                                                                              gcctggcGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCtttt                                                          >  7:20062/1‑149 (MQ=255)                                                                                     gggTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATggg                                                   <  6:91584/149‑1 (MQ=255)                                                                                           tGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTAcc                                             <  4:127446/149‑1 (MQ=255)                                                                                             gCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCg                                           <  1:293883/149‑1 (MQ=255)                                                                                              cACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCgg                                          >  2:210552/1‑149 (MQ=255)                                                                                              cACCGTTTGTCGGCGATACACTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGGTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCg                                           <  8:70334/148‑1 (MQ=255)                                                                                                     tGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGtcctcc                                    >  5:134082/1‑148 (MQ=255)                                                                                                     tGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGtcctcc                                    <  4:176589/148‑1 (MQ=255)                                                                                                       tCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTAcc                                             >  2:146894/1‑137 (MQ=255)                                                                                                       tCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTAcc                                             <  1:146894/137‑1 (MQ=255)                                                                                                          gCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGAc                              <  6:274846/149‑1 (MQ=255)                                                                                                          gCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGAc                              >  3:19454/1‑149 (MQ=255)                                                                                                                  cTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCcgc                      >  5:54053/1‑149 (MQ=255)                                                                                                                       cgaGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGt                 <  8:20062/149‑1 (MQ=255)                                                                                                                                 cTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGgcgcg       >  8:292903/1‑149 (MQ=255)                                                                                                                                    ctgTCGCTGACCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCtt    >  3:6942/3‑149 (MQ=255)                                                                                                                                    ctgTCGCTGACCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCtt    >  3:2291/3‑149 (MQ=255)                                                                                                                                     tgTCGCTGACCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAGCGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCt     >  5:76001/2‑147 (MQ=255)                                                                                                                                     tgTCGCTGACCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAGCGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCt     <  6:76001/146‑1 (MQ=255)                                                                                                                                     ggTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCttt   <  1:25413/149‑1 (MQ=255)                                                                                                                                       tCGCTGACCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCTTTg  <  4:6942/148‑1 (MQ=255)                                                                                                                                       tCGCTGACCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCTTTg  <  4:2291/148‑1 (MQ=255)                                                                                                                                              |                                                                                                                                             TTTATGTGCCCACCTCGGTGCCGGTGTTCAGCCCACAGGAAATTGCCAGCTGGTCGTGGTTGCCCTTCGACGAACTGGCCTGGCGGGTAATGGCACCGTTTGTCGGCGATACCCTCGACGAGCCTACGCTCAGGTCGCTGGTCAGCGACAGCTATCGCGGGTTCCGCCACCGCGGCATTGCGCCGTTGCAGCAGCTTGGCCATAACGAATGGATCCTGCAGCTTTTCCATGGGCCTACCCGGTCCTCCAAGGACTTTGCCGCGCAGTTGCAGGCGCGCTTTG  >  NC_002947/770402‑770683

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