Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,252,780	A→T	7.5%	L300H (CTC→CAC)	rocE ←	amino acid permease RocE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,252,780	0	A	T	7.5%	155.2 / 2.8	53	L300H (CTC→CAC)	rocE	amino acid permease RocE
Reads supporting (aligned to +/- strand):  ref base A (20/29);  new base T (2/2);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

AGCGCAAAGCACAGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACGGCAATCGCCAGCACATAG  >  NC_002947/4252636‑4252926                                                                                                                                                    |                                                                                                                                                   aGCGCAAAGCACAGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGAt                                                                                                                                                <  7:332207/149‑1 (MQ=255)  gcgcAAAGCACAGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATg                                                                                                                                               <  8:95123/149‑1 (MQ=255)      aaaGCACAGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCAGCAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCg                                                                                                                                           >  1:337976/1‑149 (MQ=255)       aaGCACAGGGTGAGGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCTACAGGCTTTTCGGTCCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCTTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGt                                                                                                                                          <  2:325704/149‑1 (MQ=255)           acaGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAgg                                                                                                                                      <  8:299299/149‑1 (MQ=255)             aGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCTGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGAt                                                                                                                                    <  7:57228/149‑1 (MQ=255)             aGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGAt                                                                                                                                    >  6:339251/1‑149 (MQ=255)                      cTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGt                                                                                                                            <  6:172775/148‑1 (MQ=255)                         aGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTtcat                                                                                                                        >  5:322258/1‑149 (MQ=255)                         aGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTtcat                                                                                                                        >  7:212490/1‑149 (MQ=255)                         aGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTtca                                                                                                                         <  1:257278/148‑1 (MQ=255)                             cccGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGGCAGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCaa                                                                                                                     <  1:314792/149‑1 (MQ=255)                                               gcTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATTCCAGTCTTTGACATTGCCCACTGCTTTTCCGCTTGGTCGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGa                                                                                                    <  1:140917/149‑1 (MQ=255)                                               gcTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATg                                                                                                  >  7:137725/1‑149 (MQ=255)                                                   gCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGa                                                                                              >  3:58089/1‑149 (MQ=255)                                                    cTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGa                                                                                              <  6:322258/148‑1 (MQ=255)                                                    cTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGa                                                                                              <  3:362799/148‑1 (MQ=255)                                                     tCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGAc                                                                                             >  3:273845/1‑148 (MQ=255)                                                       aGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGAcc                                                                                            <  4:109711/147‑1 (MQ=255)                                                         cggcgACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCa                                                                                           <  4:325843/146‑1 (MQ=255)                                                         cggcgACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCa                                                                                           >  3:325843/1‑146 (MQ=255)                                                               cAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAaca                                                                                  >  1:162743/1‑149 (MQ=255)                                                                           tgccatgccaGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACg                                                                      <  1:258052/149‑1 (MQ=255)                                                                             ccatgccaGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACgg                                                                     <  8:238317/148‑1 (MQ=255)                                                                                  ccaGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGTGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTc                                                               >  7:403546/1‑149 (MQ=255)                                                                                  ccaGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGTGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTc                                                               >  7:397876/1‑149 (MQ=255)                                                                                  ccaGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCttt                                                                <  4:273845/148‑1 (MQ=255)                                                                                  ccaGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTc                                                               >  4:60176/1‑149 (MQ=255)                                                                                        ttGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGATTTCCATCAg                                                         >  8:177535/1‑149 (MQ=255)                                                                                             cATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCgg                                                    >  1:366769/1‑149 (MQ=255)                                                                                              aTGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGc                                                   >  4:170233/1‑149 (MQ=255)                                                                                                   ccA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCt                                              <  5:151531/149‑1 (MQ=255)                                                                                                          ggATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGc                                         <  7:188648/149‑1 (MQ=255)                                                                                                             tACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGc                                      <  8:212490/149‑1 (MQ=255)                                                                                                              aCGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGca                                     >  5:197818/1‑149 (MQ=255)                                                                                                                gcgTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGc                                               <  2:362247/137‑1 (MQ=255)                                                                                                                gcgTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGc                                               >  1:362247/1‑137 (MQ=255)                                                                                                                gcgTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGcac                                    >  2:287912/1‑148 (MQ=255)                                                                                                                gcgTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGcac                                    >  6:349114/1‑148 (MQ=255)                                                                                                                gcgTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGcac                                    >  5:374794/1‑148 (MQ=255)                                                                                                                 cgTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACaa                                  <  2:162743/149‑1 (MQ=255)                                                                                                                  gTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAAt                                 <  7:253048/149‑1 (MQ=255)                                                                                                                   tGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATg                                >  1:921/1‑149 (MQ=255)                                                                                                                     gAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGc                              <  2:337976/149‑1 (MQ=255)                                                                                                                      aGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGcc                             <  4:58089/149‑1 (MQ=255)                                                                                                                          aTACAACCCGG‑AGTTGCCCACCGAGTGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACa                         <  8:397876/149‑1 (MQ=255)                                                                                                                          aTACAACCCGG‑AGTTGCCCACCGAGTGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACa                         <  8:403546/149‑1 (MQ=255)                                                                                                                          aTACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACa                         <  3:132417/149‑1 (MQ=255)                                                                                                                                cccGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACgg                   <  3:317121/149‑1 (MQ=255)                                                                                                                                cccGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACgg                   <  5:339251/149‑1 (MQ=255)                                                                                                                                           cccACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACGGCAATCGCCAg         <  1:287912/149‑1 (MQ=255)                                                                                                                                           cccACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACGGCAATCGCCAg         <  7:177535/149‑1 (MQ=255)                                                                                                                                              aCCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACGGCAATCGCCAGca       >  5:159373/1‑148 (MQ=255)                                                                                                                                                  agagGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACGGCAATCGCCAGCACATag  <  2:921/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   AGCGCAAAGCACAGGGTGATGCTCAGCGCCCGCAGCGGCACGCCACGCTTGCTCAGCGGCGACAGGCTTTTCGGTGCCATGCCAGTCTTGGACATGGCCCA‑‑GAGGATACGCGTGGAGGCATACAACCCGG‑AGTTGCCCACCGAGAGGATGGCCGTGAGGATGACGAAGTTCATCAAGTCGGCGGCGTAAGGGATGCCGACCATGTCGAACACCTGCACGAACGGGCTTTCCATCAGCCCGGCCTGCTCGTGCGGCACAATGGCCGACAGCACGGCAATCGCCAGCACATAG  >  NC_002947/4252636‑4252926

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: ‑