Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,708,363	T→C	9.8%	M171V (ATG→GTG)	actP‑III ←	acetate permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,708,363	0	T	C	9.8%	139.5 / 4.8	51	M171V (ATG→GTG)	actP‑III	acetate permease
Reads supporting (aligned to +/- strand):  ref base T (24/22);  new base C (2/3);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 6.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGCCCTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGCCACCAGGTACATCAGCGCCACCAC  >  NC_002947/3708217‑3708498                                                                                                                                                    |                                                                                                                                        cTGGCCCTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGc                                                                                                                                       <  2:283630/149‑1 (MQ=255)    gCCCTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGCTGATCTGCACCCA‑GGTGGTGGCGAGCATGCCAc                                                                                                                                    >  1:30636/1‑149 (MQ=255)    gCCCTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCa                                                                                                                                     <  2:258153/148‑1 (MQ=255)      ccTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGTCAcct                                                                                                                                  >  8:289347/1‑148 (MQ=255)      ccTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCATGCTCGCCAcca                                                                                                                                  <  6:31770/149‑2 (MQ=255)           gCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCAGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGt                                                                                                                             <  2:66680/149‑1 (MQ=255)            cATGCACGGCCACCGCAATGTCAAACATGGCCTAGTTGCTGAAGCCGAAGTGCTTGAGCACGATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGAGGATCTGCACCCA‑GTTTGTGGCGAGGATGCCACCGAAGGTg                                                                                                                            <  8:57012/149‑1 (MQ=255)               gCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACa                                                                                                                         >  3:248762/1‑149 (MQ=255)                 aCGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACa                                                                                                                         >  4:64795/1‑147 (MQ=255)                      cACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGaaa                                                                                                                  <  3:258522/149‑1 (MQ=255)                       aCCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAAc                                                                                                                 <  5:51001/149‑1 (MQ=255)                           cACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCAt                                                                                                              >  1:82205/1‑148 (MQ=255)                                gCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCAt                                                                                                                                         >  3:187830/1‑116 (MQ=255)                                gCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCAt                                                                                                                                         <  4:187830/116‑1 (MQ=255)                                  aaaCATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCAccc                                                                                                      >  3:38120/1‑149 (MQ=255)                                   aaCATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCAcccc                                                                                                     >  7:208131/1‑149 (MQ=255)                                          ccTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGc                                                                                              <  7:106894/149‑1 (MQ=255)                                               gTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGG‑CATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACg                                                                                        <  6:284707/149‑1 (MQ=255)                                                 gCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACgg                                                                                       >  8:253601/1‑149 (MQ=255)                                                   tGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCCGCACCCCGACCAGCATCACGGCg                                                                                     >  3:288167/1‑149 (MQ=255)                                                    gAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCg                                                                                     >  5:199048/1‑148 (MQ=255)                                                    gAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCATGCTCGCCAcca                                                                                                                                  >  5:313263/1‑102 (MQ=39)                                                    gAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCATGCTCGCCAcca                                                                                                                                  <  6:313263/103‑2 (MQ=39)                                                     aaGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGa                                                                                                                    >  5:169290/1‑116 (MQ=255)                                                     aaGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGa                                                                                                                    <  6:169290/116‑1 (MQ=255)                                                        ccGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAg                                                                                <  6:306805/149‑1 (MQ=255)                                                        ccGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAg                                                                                >  5:306805/1‑149 (MQ=255)                                                         cGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAgg                                                                               <  6:199048/149‑1 (MQ=255)                                                            aGTGCTTGAGCACCATGAACGCCATGTAACTGGTGCCTGATAGCATGATTACCGCCTTGATGATCTGCACCCA‑GGTTGTGGCGATCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAg                                                                            <  1:94203/149‑1 (MQ=39)                                                             gTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCACGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGc                                                                           >  1:247057/1‑149 (MQ=255)                                                                   gAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATg                                                                      <  4:248762/148‑1 (MQ=255)                                                                       aCCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGCCCAGCATCACGGCGTACAGGTAGCTGATGCCGaa                                                                 >  5:269451/1‑149 (MQ=255)                                                                       aCCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGaa                                                                 <  3:123621/149‑1 (MQ=255)                                                                           tGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAAcag                                                              >  6:97287/1‑148 (MQ=255)                                                                                  cATGAAACTGGTGAATGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAAACATCAGCACACCGACCACCATCACGGCGTACAGTTAGCTGATGCCGAACAGCAGCTCg                                                       >  8:147360/1‑148 (MQ=38)                                                                                    tGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATc                                                    <  7:253601/149‑1 (MQ=255)                                                                                         cTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCtt                                               <  3:64795/149‑1 (MQ=255)                                                                                          tGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCAGGGTGGTGGCGAGCATGCCACCGAAGGt                                                                                                                             >  1:62319/1‑71 (MQ=255)                                                                                          tGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGt                                                                                                                             <  2:62319/70‑1 (MQ=255)                                                                                              gCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGACGAACAGCAGCTCGATCAGCTTGc                                             >  2:84684/1‑146 (MQ=255)                                                                                                   aTAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGcc                                      >  8:262708/1‑148 (MQ=255)                                                                                                      gcagcaTTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCAc                                                                                                                                    <  6:276756/51‑1 (MQ=255)                                                                                                      gcagcaTTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCAc                                                                                                                                    >  5:276756/1‑51 (MQ=255)                                                                                                        atcaTTACAGCCTTTATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCAt                                <  4:38120/147‑1 (MQ=255)                                                                                                               ccGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTgcgc                          >  2:237739/1‑148 (MQ=255)                                                                                                                cGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGcca                        >  8:141406/1‑149 (MQ=255)                                                                                                                  ccTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGccac                       >  8:23182/1‑148 (MQ=255)                                                                                                                               cACCCA‑GGTGGTGGCGAGCACGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGCCACCAGGTACATCa            <  2:247057/146‑1 (MQ=255)                                                                                                                                 cccA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGCCACCAGGTACATCAGCGcc       <  5:97287/149‑1 (MQ=255)                                                                                                                                  ccA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAgcgc                                       <  6:298847/116‑1 (MQ=255)                                                                                                                                  ccA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAgcgc                                       >  5:298847/1‑116 (MQ=255)                                                                                                                                  ccA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGCCACCAGGTACATCAGCGcca      >  7:221058/1‑149 (MQ=255)                                                                                                                                       gtggtgGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGCCACCAGGTACATCAGCGccaccac  <  7:141406/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                        CTGGCCCTTGGCATGCACGGCCACCGCACTGGCAAACATGGCCTCGGTGCTGAAGCCGAAGTGCTTGAGCACCATGAAGGCCATGAAACTGGTGCCTGATAGCAGCATTACCGCCTTGATGATCTGCACCCA‑GGTGGTGGCGAGCATGCCACCGAAGGTGACATAGGAAACCATCAGCACCCCGACCAGCATCACGGCGTACAGGTAGCTGATGCCGAACAGCAGCTCGATCAGCTTGCCAGCGCCGACCATTTGCGCCACCAGGTACATCAGCGCCACCAC  >  NC_002947/3708217‑3708498

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: ‑