Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,055	C→T	T85T (ACC→ACT)	thrB →	homoserine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,055	0	C	T	96.7%	83.6 / ‑4.2	30	T85T (ACC→ACT)	thrB	homoserine kinase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (13/16);  total (14/16)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.75e-01

CCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCA  >  NC_000913/2818‑3288                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                          cccGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAata                                                                                                                                                                                                                              <  1:13191/251‑1 (MQ=255)   cgtgtcccAGGGCCTATATGAGCGTTGGGTTTGAGGTGATCTGGGCGGCGTTGACCGCTGTTGATGTTGCATTGATCGGAGATGTAGTCACGGTTGAGGCGGCAGAGCCATTCAGCTTGAACAACCTCGGACGCTTTGCCGATAAGCTGTCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCGGGGAGCGTTTTTGCAAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATg                                                                                                                                                                                                                            <  2:186355/245‑1 (MQ=255)          cAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCg                                                                                                                                                                                                                     >  1:60349/1‑251 (MQ=255)                 aaTATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGCAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATAAGCCAATCGGTTCggg                                                                                                                                                                                                              >  1:37420/1‑251 (MQ=255)                     ggAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTa                                                                                                                                                                                                          <  1:290552/250‑1 (MQ=255)                          gTCGGGTTTGCTGTGCTCGGGGCTGCGTTGATACCTGTTGTTGGTGCATTGCACGGTGATGTAGTCACGGTTGAGGCGGCAGAGACATTCATTCTCAACAACCTAGGACGCTGTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTCTCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCTATGACTCTGAAAAAGAATAGGCCAATCGGTTCGTGCTTAGGCTc                                                                                                                                                                                                     <  2:328350/251‑1 (MQ=255)                            cGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTcc                                                                                                                                                                                                    >  1:207841/1‑250 (MQ=255)                                            ggggCGGCGGTGACCCCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGGAAATATCGTTTTTCAGTGCTGGGAGCGGTTTTGCCAGGAGCTTGGAAAGCAAATTCCAGTGGCGGTGACTCTGGTACAGAATAAGACAACCGGTTCGGGCTTAGGCTcccgcgccggttccggggg                                                                                                                                                                                   >  2:167861/1‑234 (MQ=255)                                                             tGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCgg                                                                                                                                                                  >  1:5604/1‑250 (MQ=255)                                                                 gaggggtatttGCTAGGAGATGTAGTCACGGTTGAGGCGGCAGAGACAGTCAGTCTCAACACCCTCGGACGCTGGGCCGATAAGCTGCCGTCAGAACCACGGTAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCGCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGatgaa                                                                                                                                                              <  2:174256/242‑1 (MQ=255)                                                                   gggTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGCTGATGGCGatgaatg                                                                                                                                                            <  1:57202/250‑1 (MQ=255)                                                                          ttGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAACTATCGTTTATCAGTGCTGGGGGCGTTTTTGCCAGGAGCTTGGCAAGCAAATTCCAGTGGCGATGACTCTGGAAAAGAATATGCCAATCGGTTCGGGCTTAGGCTCCAGCGCCTGTTCGGTGGTCGCGGCGGTGATGGCGTTGAATGAACACTg                                                                                                                                                     >  1:255789/1‑251 (MQ=255)                                                                                 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)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                          CCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCA  >  NC_000913/2818‑3288

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: ‑