Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,786,965	C→T	A50T (GCC→ACC)	ppsA ←	phosphoenolpyruvate synthetase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,786,965	0	C	T	96.9%	82.5 / ‑6.3	32	A50T (GCC→ACC)	ppsA	phosphoenolpyruvate synthetase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (7/24);  minor base G (1/0);  total (8/24)
Fisher's exact test for biased strand distribution p-value = 2.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GGCGGAGGAGCGCACCGCAAAAGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGCGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATCTTTGCATATTTAACCGGATGAAAAAAACGGTGAATCGTTC  >  NC_000913/1786723‑1787210                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      ggCGGAGGAGCGCACCGCAAAAGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCAt                                                                                                                                                                                                                                               <  2:147552/251‑1 (MQ=255)    ggaggaGCGCACCGCAAAAGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTcg                                                                                                                                                                                                                                            <  1:304275/251‑1 (MQ=255)     gaggagCGCACCGCCAAAGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATATGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAACCCATTcgg                                                                                                                                                                                                                                           <  2:418435/251‑1 (MQ=255)        gagCGCACCGCAAAAGAGGCGTTTTCGTCAACGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTcggaac                                                                                                                                                                                                                                        <  2:520631/251‑1 (MQ=255)         agCGCACCGCAAAAGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTcggaacg                                                                                                                                                                                                                                       <  1:161285/251‑1 (MQ=255)          ccgcACCGCAAACGAGGCGTTGTCGGCATCGTCGGAAACCTGTGCATAGTCTTCGCGGATGGCTTTTGCCAGCTCAGGCTGGAAGGGAGTGGCGATAATCCACTGGCGGATGTGCTCGCCCGCTTTCGCAAGCTGAGGAACATCGTCAATATCCGTTGTATCCAGCAGTTCATAAATTCGC‑GGTGTTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGACTGTGGTGAAACCATTcggaacgg                                                                                                                                                                                                                                      <  2:204025/250‑1 (MQ=255)                     aaGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTTCGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCAtt                                                                                                                                                                                                                           <  1:87372/251‑1 (MQ=255)                           cGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGaa                                                                                                                                                                                                                     <  2:361147/251‑1 (MQ=255)                                           ggAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGCAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCAATCGGAACGGAAACACCCCTTCCCGACAGCTTAGAAAACAttt                                                                                                                                                                                                     >  2:235586/1‑251 (MQ=255)                                             aaaGCGGTGCATATGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGAGAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCTGAAAGATTAGTAATCATTTCa                                                                                                                                                                                                   <  2:353130/251‑1 (MQ=255)                                                                                aGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTAc                                                                                                                                                                <  2:438133/251‑1 (MQ=255)                                                                                     aGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTGCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTAcatcat                                                                                                                                                           <  2:75663/251‑1 (MQ=255)                                                                                                 aGTGTCGATAATCCGCTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGtt                                                                                                                                               <  2:442371/251‑1 (MQ=255)                                                                                                 aGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCCTTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGtt                                                                                                                                               >  1:514912/1‑251 (MQ=255)                                                                                                                                        cGCAAGTTGAGTAACATCGTCAATATCCGGTTTATCCAGCAGTTAATAAATGCGCTGGT‑TTACGCCGCTTTGGGCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACCCCAATTCCGGAAATATTAGTAATCATTTCACCTAGGGAGGCATTTTTGCCCCCATCCCTGTCTACATAATTCATGCCGTGTTGGTTATACCAAAGCACCAGCGGGGCCGAGCCATTGTTgg                                                                                                        <  2:308807/251‑1 (MQ=255)                                                                                                                                                gAGTAACACCGTCAATATCCCTTTTATCCAGCAGTTCATAAATGCGCGGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAACGATTAGTAATCATTTCACCCAGGGAGGCAGTTTTGCCCCCAACCCTGTCTACATCAGTCATGCCGAGTTGGTTATACCAAAGCACGGGCGGTGAGGAGCCATTGTTGGACATCGa                                                                                                 <  2:263435/250‑1 (MQ=255)                                                                                                                                                    aaCATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCAAGAAACTGGTTAAACGCGTCGGCGGTTGGGGTGAAACCATTCGGAACGGAAAAACCCCTTCCGGGAAGGTTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCCACCCTGTCTACATCCTTCATGCCGAGGTGGTTCTACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGTACaa                                                                                             >  2:448367/1‑250 (MQ=255)                                                                                                                                                      catctacAATAACCGTTGTATCCAGCAGCTCATAAAGGCGCTGGT‑TTTCGCCGATTTGGTGCAGAAACTGGTTAAACGCGTCGGCGGTTGTGTTGAAACCATTCGGAACGTAAACACCCATTCCGGAAATATTAGTAATCATTTCTCCCAGGGTGGCTTTTTTGCCCCCAACCCTGTCGACACCATTCATGCCTAGTTGTCTATATCAAATCACCAGCGGTGTCGAGCCATTGTTGGACATCGAACAATcc                                                                                          <  2:314851/245‑1 (MQ=255)                                                                                                                                                               tatCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGc                                                                                                                                                     <  2:423041/183‑1 (MQ=255)                                                                                                                                                               tatCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAAAGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCCTTCATGc                                                                                                                                                     >  1:423041/1‑183 (MQ=255)                                                                                                                                                                  ccGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGGGAAACCCTTCGGAACGGAAACACCCCATCCGGACAGATTAGTAATCATTTCACCCAGGGCGGCATTTTTTCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAACGGGGACGAGCCCTTGTTGGACATCGAACAATCCTATTGTGATaa                                                                               >  1:366858/1‑250 (MQ=255)                                                                                                                                                                   cGTTTTATCCAGCAGTTAATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGGACGGGAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCCGTATACATCCTTCCTGCCGAGTTGGTTATACCAAAACCCCAGCGGGGGCAGGCCATTGTTGGGCCTCGAAAAATCCTTTTGTGGTAAAt                                                                             >  2:45739/1‑251 (MQ=255)                                                                                                                                                                                 gTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGaa                                                               <  1:235586/251‑1 (MQ=255)                                                                                                                                                                                               tGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCCGCGGTGACGAGCCATTGTTGGACATCGAAAAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTgcgc                                                 >  2:94714/1‑251 (MQ=255)                                                                                                                                                                                                  t‑ttACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAAATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTTATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTTTTGGACATCGAACAATCCTTTTTTGATTAATGAACGGTTTTAGTAACACAATTCttcgtatt                                              >  1:218770/1‑244 (MQ=255)                                                                                                                                                                                                     tACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCCCCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACAGCCTTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACTAGCCATTGTGGGACATCGAACAATCCTTTTGTGATAAATGAACTGTTTGAGAAACACATTGCTGCGCAttg                                             <  2:384934/250‑2 (MQ=255)                                                                                                                                                                                                       cgccgcTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATc                                          <  2:472289/251‑1 (MQ=255)                                                                                                                                                                                                       cgccgcTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATc                                          <  2:514912/251‑1 (MQ=255)                                                                                                                                                                                                        gccgcTTTGTTCCAGAAACTTGTTAAACTCGTCGTCGGTTGTGGTTAACCCATTCGGAACGGAAACCCCCATTCCGGAAAGATTAGTAATCAGTTCACCCATGGAGGCATTTTTCCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACTTGCGGTGACGAGCCATTGTTGGACATCTAACAAGTCTTCTGTGATAAATGAACGGTTTGAGCAACACATTTCTGCGCAGTTATCt                                         <  1:396947/251‑1 (MQ=255)                                                                                                                                                                                                                    cAGAAACTGGTTAAACGCGGCGGCGGTTGTGGTGAAACCATTCGGAACGGAAACACCCATGCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACAGTTCTGCGCATTTATCTTTGCAGATTTaa                             <  2:104781/251‑1 (MQ=255)                                                                                                                                                                                                                                     cgTCGGCGGTTGTGGTGAAACCATTCGGAACGGAGACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATCTTTGCATATTTAACCGGATGAAAAAAACgg            <  1:308452/251‑1 (MQ=255)                                                                                                                                                                                                                                           cggTTGTGGTGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATCTTTGCATATTTAACCGGATGAAAAAAACGGTGAATc      <  1:143570/251‑1 (MQ=255)                                                                                                                                                                                                                                                gtggtgAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATCTTTGCATATTTAACCGGATGAAAAAAACGGTGAATCGTTc  >  1:129807/1‑250 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      GGCGGAGGAGCGCACCGCAAAAGAGGCGTTTTCGTCATCGGCGGAAAGCTGTGCATAGGCTTCGCGGATGGCGTTTTCCAGCTCAGGCTGGAAGGGAGTGTCGATAATCCACTGGCGGATTTGCGCGCCCGCTTTCGCAAGCTGAGTAACATCGTCAATATCCGTTTTATCCAGCAGTTCATAAATGCGCTGGT‑TTACGCCGCTTTGGTCCAGAAACTGGTTAAACGCGTCGGCGGTTGTGGCGAAACCATTCGGAACGGAAACACCCATTCCGGAAAGATTAGTAATCATTTCACCCAGGGAGGCATTTTTGCCCCCAACCCTGTCTACATCATTCATGCCGAGTTGGTTATACCAAAGCACCAGCGGTGACGAGCCATTGTTGGACATCGAACAATCCTTTTGTGATAAATGAACGGTTTGAGAAACACATTTCTGCGCATTTATCTTTGCATATTTAACCGGATGAAAAAAACGGTGAATCGTTC  >  NC_000913/1786723‑1787210

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑