Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,068,774	C→T	7.5%	A356T (GCA→ACA)	rutG ←	pyrimidine permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,068,774	0	C	T	7.5%	157.5 / 2.9	53	A356T (GCA→ACA)	rutG	pyrimidine permease
Reads supporting (aligned to +/- strand):  ref base C (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 = 4.11e-01

CCAGCGTGAGAGCAAAATCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGATATTTTCAGCA  >  NC_000913/1068630‑1068919                                                                                                                                                 |                                                                                                                                                  ccAGCGTGAGAGCAAAATCACCCGCGCCCAGCACTAAGTTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGcacca                                                                                                                                               >  2:276515/1‑149 (MQ=255)  cAGCGTGAGAGCAAAATCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGcaccac                                                                                                                                              <  6:167171/149‑1 (MQ=255)   aGCGTGAGAGCAAAATCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCaccacc                                                                                                                                             <  2:95442/149‑1 (MQ=255)             cAAAATCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACcgcg                                                                                                                                   >  6:355732/1‑149 (MQ=255)              aaaaTCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCgg                                                                                                                                  >  5:115871/1‑149 (MQ=255)               aaaTCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGc                                                                                                                                 <  5:355732/149‑1 (MQ=255)                  tCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCg                                                                                                                               >  7:92000/1‑148 (MQ=255)                    aCCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGGCGGaa                                                                                                                            <  8:362305/149‑1 (MQ=255)                      ccGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATg                                                                                                                          <  2:289996/149‑1 (MQ=255)                       ggcgcCCAGCACTAAGGTTACTGCGACAATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTCCCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATgg                                                                                                                         <  5:282232/148‑1 (MQ=255)                       cgcgCCCCGCACTACGGTGACTGCGACAATACTCAAATTCCCGTTCTGGCTTAAATCGACACGGTGTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCACTACCCGCGGCCGGAATgg                                                                                                                         <  5:277394/149‑1 (MQ=255)                            ccAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGa                                                                                                                    <  1:276515/149‑1 (MQ=255)                                   tAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGTACCACCAATAACCGCGGCCGGAATGGTATGAATCAgcg                                                                                                             >  5:238269/1‑149 (MQ=255)                                   tAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGTACCACCAATAACCGCGGCCGGAATGGTATGAATCAgcg                                                                                                             >  5:233108/1‑149 (MQ=255)                                            tGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAAtt                                                                                                    >  5:48410/1‑149 (MQ=255)                                                 ccATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGt                                                                                               <  8:92000/149‑1 (MQ=255)                                                 ccATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGt                                                                                               <  6:48410/149‑1 (MQ=255)                                                   aTAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGTACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGa                                                                                             <  6:238269/149‑1 (MQ=255)                                                   aTAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGTACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGa                                                                                             <  6:233108/149‑1 (MQ=255)                                                   aTAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTg                                                                                              >  1:177226/1‑148 (MQ=255)                                                         aaaTTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCCGCCCGAACACCACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGGGAAAAGcc                                                                                       <  2:278970/149‑1 (MQ=255)                                                           aTTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCa                                                                                     <  8:276257/149‑1 (MQ=255)                                                                 gTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCa                                                                               <  7:326348/149‑1 (MQ=255)                                                                 gTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCa                                                                               <  6:115871/149‑1 (MQ=255)                                                                 gTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCa                                                                               <  5:342364/149‑1 (MQ=255)                                                                         ttAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGcaccac                                                                                                                                              <  6:21017/78‑1 (MQ=255)                                                                         ttAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGAt                                                                        >  3:147898/1‑148 (MQ=255)                                                                                 acacGGTTTTGTACCCATATCCTTGCGCCTTCGACGTCAATCAGCCCTAACACAACAATTGATGCACCACCACTAACCGCGGCCGGAATGGTATGAATCAGCTCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGgcagc                                                               <  2:202609/149‑1 (MQ=255)                                                                                   acGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAAt                                                                                                                  <  1:35862/96‑1 (MQ=255)                                                                                   acGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAAt                                                                                                                  >  2:35862/1‑96 (MQ=255)                                                                                     ggTTTTGTACCCATATCCTTGCGCCTGCGACTGCAAGCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTAAGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGAt                                                                        <  4:46496/136‑1 (MQ=255)                                                                                     ggTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCTAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATCGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGAt                                                                        >  3:46496/1‑136 (MQ=255)                                                                                     ggTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGgcagcagc                                                            >  7:305050/1‑148 (MQ=255)                                                                                         ttGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGcaaca                                                        >  4:317985/1‑148 (MQ=255)                                                                                               ccATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCGCCAAATTTCGGTGAAAAGccc                                                                                      <  5:231207/112‑1 (MQ=255)                                                                                               ccATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCGCCAAATTTCGGTGAAAAGccc                                                                                      >  6:231207/1‑112 (MQ=255)                                                                                                  tatCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCg                                              >  4:79875/1‑149 (MQ=255)                                                                                                  tatCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCg                                              >  5:202860/1‑149 (MQ=255)                                                                                                  tatCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGAGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCg                                              >  2:107370/1‑149 (MQ=255)                                                                                                    tCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTc                                            <  7:169529/149‑1 (MQ=255)                                                                                                      cTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGa                                          <  3:79875/149‑1 (MQ=255)                                                                                                         gctccTTCGACGGCAATCAGCCAGAACACAACAATTGATGCACCACCAATAAACGAGTCCGGAATGGTATGAATAAGCGCACCAAATTTCGGTGAAAAGAACAACATCATGTCGATTACTGCATCAGCAAAAAACACCAGCGTCGat                                         <  8:305050/144‑2 (MQ=255)                                                                                                                cGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTg                                <  1:107370/149‑1 (MQ=255)                                                                                                                              ccGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATca                   >  2:70472/1‑148 (MQ=255)                                                                                                                                gAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCacac                <  3:317985/149‑1 (MQ=255)                                                                                                                                   cacaACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCa                                                                               >  2:153231/1‑83 (MQ=255)                                                                                                                                   cacaACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCa                                                                               <  1:153231/83‑1 (MQ=255)                                                                                                                                    acaacaATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCCGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGa             >  3:244086/1‑148 (MQ=255)                                                                                                                                      aacaaTTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTg                                >  1:217097/1‑127 (MQ=255)                                                                                                                                      aacaaTTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTg                                <  2:217097/127‑1 (MQ=255)                                                                                                                                      aacaaTTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGatat          >  8:184631/1‑149 (MQ=255)                                                                                                                                      aacaaTTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGatat          >  4:86968/1‑149 (MQ=255)                                                                                                                                          aTTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAAGAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGATATTTTc      <  4:147898/149‑1 (MQ=255)                                                                                                                                           ttGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGATATTTTCa     <  6:202860/149‑1 (MQ=255)                                                                                                                                           ttGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGATATTTTCa     <  3:86968/149‑1 (MQ=255)                                                                                                                                              aTGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGATATTTTCAGCa  <  2:177226/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                  CCAGCGTGAGAGCAAAATCACCCGCGCCCAGCACTAAGGTTACTGCGACCATAATCAAATTACCGTTCTGGCTTAAATCGACACGGTTTTGTACCCATATCCTTGCGCCTGCGACGGCAATCAGCCCGAACACAACAATTGATGCACCACCAATAACCGCGGCCGGAATGGTATGAATCAGCGCACCAAATTTCGGTGAAAAGCCCAACAGCATGGCGATGACGGCAGCAGCAACAAACACCAGCGTCGAGTAGACTTTGGTCACGGCCATCACACCGATATTTTCAGCA  >  NC_000913/1068630‑1068919

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑