Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,142	C→T	C114C (TGC→TGT)	thrB →	homoserine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,142	0	C	T	93.3%	79.6 / ‑6.5	31	C114C (TGC→TGT)	thrB	homoserine kinase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  major base T (11/17);  minor base G (1/1);  total (13/18)
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

GAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCAGGGCTATTTTACCG  >  NC_000913/2898‑3376                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                           gggtggtaggtaCGGTTGAGGCGGCAGAGACATTCAGGCGCAACAACCTCGGACGCTTGGCCGATAAGCGGCCGTCAGAACCACGGGAAAATATCGTTTACCAGGGCTTGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATTCCAATCGGTTCGGGCGTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAg                                                                                                                                                                                                                                      <  2:314631/240‑1 (MQ=255)        aGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAGGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCtt                                                                                                                                                                                                                                <  1:60902/250‑1 (MQ=255)         gTCACGGGTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGTAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTTGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTaa                                                                                                                                                                                                                              <  1:228301/251‑1 (MQ=255)                                aTTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGAAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGAAACTCGTTTGCTGGCTTTg                                                                                                                                                                                                        >  1:249051/1‑250 (MQ=255)                                  tCAGTCTCAACAACCTCGGACGTTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCATTTGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGTTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACGGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGAt                                                                                                                                                                                                      <  2:320071/250‑1 (MQ=255)                                         acacaacCTCGGGCGCTGTGCCGGTAAGCTGCCGTCAGAACCATGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAg                                                                                                                                                                                               <  2:11774/248‑1 (MQ=255)                                             aacCTCGGACGCTTTGCCGATAAGCTGCTGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCTTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGa                                                                                                                                                                                          <  1:307009/251‑1 (MQ=255)                                                           ttccGATAAGCCGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTTGGAGCGTTGTTGCCAGGAGCTTTGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGTCACTCGTTTGCTTGCTTTGATGGGCGAGCTGGAAgtacgaatctcc                                                                                                                                                                             <  2:364497/248‑12 (MQ=255)                                                               gATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGgc                                                                                                                                                                          >  1:248367/1‑249 (MQ=255)                                                                                 ccACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGt                                                                                                                                                      <  1:239105/251‑1 (MQ=255)                                                                                       gcaaaTATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGACAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGCCAAGCCGCTTAATGACACCCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCCTTCATTACGACAACGTGGCAcc                                                                                                                                                >  2:116847/3‑251 (MQ=255)                                                                                         aaaTATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCgt                                                                                                                                              >  1:368578/1‑251 (MQ=255)                                                                                          aaTATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCgtg                                                                                                                                             >  1:265228/1‑251 (MQ=255)                                                                                          aaTATCGTTTATAAGTGATGGGAGCGTTTTTGCCAGGAGCTTGGAAAGCAAATTCCAGTGGCGCTGACTCTGGAAAAGAATATGCCAATAAGTTCGGGCTTAGGCTCCAAAGCCTGTGCGGTGGACGCGGAGCTGATGGCGATGAATGAACACTGGGGCAGGCGGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGCGCTGGAAGGACGAATATCCGGCAGCAGTCATTACGACaatgatacaccg                                                                                                                                               >  1:299711/1‑239 (MQ=255)                                                                                               cGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGtttt                                                                                                                                         <  1:78269/250‑1 (MQ=255)                                                                                                              ggAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGAAGt                                                                                                                         >  1:232366/1‑251 (MQ=255)                                                                                                                         gCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCga                                                                                                               >  1:142000/1‑250 (MQ=255)                                                                                                                                             aTTCCAGTTGCGATGTCTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATcagcca                                                                                          <  1:138441/251‑1 (MQ=255)                                                                                                                                                                 ggAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTtgatg                                                                      <  1:308905/251‑1 (MQ=255)                                                                                                                                                                 ggAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTtgatg                                                                      >  1:15593/1‑251 (MQ=255)                                                                                                                                                                         atatGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCtg                                                              >  1:237543/1‑251 (MQ=255)                                                                                                                                                                           atGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCtgtg                                                            <  1:324951/251‑1 (MQ=255)                                                                                                                                                                           atGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGCGGTCGCGGCGCTGATGGAGATGAATGAACACTGTGGAAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGCTGAGTGGCtgtg                                                            >  1:227867/1‑251 (MQ=255)                                                                                                                                                                           atGCCAATCGGATCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACAATGTGGCAAGCCGCTTAATGACCCTCGATTGCTGGCTTTGCTGGGCGAGCTGGACGGACGAATATCCGGCAGCATTCATTACGCCAACGTGGCAca                                                                                                                                                >  1:351444/1‑166 (MQ=255)                                                                                                                                                                                    ggTTCGGTGTTAGGCGCCAGCGCCTTTTCGGTGGTCGCGGCGCTGATGGTGATGCATGAACACTGTGGCAAGCCGCTTAATGACTCTCGTTTGCTGGTTGTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGTCACCGTGTTTTCGTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTgga                                                   <  2:265228/251‑2 (MQ=255)                                                                                                                                                                                        cGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTAt                                               <  1:329010/251‑1 (MQ=255)                                                                                                                                                                                        cGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTAt                                               <  1:167861/251‑1 (MQ=255)                                                                                                                                                                                              caggcgcccgcggctggtCGGTGGTTGCCGCGCTGAGTGTGATGAATGAACACTTGGACCAGCCGATGTATGACCCTCTCTTGCTGGCGTTGATGGGCGAGCTGGAAGGACGAATCGCCGGAAGCATTCATTACGACAACGTGGCACCGTGTTTTCTGGGTGGTAGGCAGTTGATGATCGAGGAAAACGACATCATCAGCCAGCAAGTGCCATGTTTTTATTAGTGGCTGTGGGTGCTGGCGTATCCgggg                                         <  2:117102/234‑1 (MQ=255)                                                                                                                                                                                               aGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGGATCCgggg                                         >  1:253234/1‑250 (MQ=255)                                                                                                                                                                                                                    gggcgctgctcTGATGGCGATGAATGAACACTTTGGCACGCCTCTTAATGACACTCGTTTGCTGGCTTGGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGGTATGCAGTTGATGAGCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAg                   <  1:152565/241‑1 (MQ=255)                                                                                                                                                                                                                                     cGATGAATGAACACTGTGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGACGAATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTTGGTGTTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCAGGGCTATTTTACCg  <  1:165206/251‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                           GAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCAGGGCTATTTTACCG  >  NC_000913/2898‑3376

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑