Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,181,995	G→A	L279L (CTG→TTG)	potD ←	spermidine preferential ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,181,995	0	G	A	96.9%	99.4 / ‑7.0	32	L279L (CTG→TTG)	potD	spermidine preferential ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (17/14);  minor base C (0/1);  total (17/15)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

AACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAGCAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAGTTTTTTCAGCTCG  >  NC_000913/1181750‑1182239                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                     aaCGGGCGGTAATACCACCGCCCGCTTGTTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGa                                                                                                                                                                                                                                                 <  1:226543/251‑1 (MQ=255)  aCGGGCAGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGaa                                                                                                                                                                                                                                                <  2:241430/251‑1 (MQ=255)   cGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGa                                                                                                                                                                                                                                                 >  1:111258/1‑249 (MQ=255)                                                      tCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCg                                                                                                                                                                                              <  1:158867/249‑1 (MQ=255)                                                      tCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGc                                                                                                                                                                                             <  2:111258/250‑1 (MQ=255)                                                                 tctTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGtcaat                                                                                                                                                                                 >  1:539490/1‑248 (MQ=255)                                                                 cctTCATAAATGCTGCTGGCTGCGCCACCGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGtccat                                                                                                                                                                                 <  2:153190/250‑1 (MQ=255)                                                                  ctTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGtccatc                                                                                                                                                                                >  1:308177/1‑251 (MQ=255)                                                                             ctgctgGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATgcc                                                                                                                                                                     >  2:471194/1‑251 (MQ=255)                                                                                  ggctgCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCct                                                                                                                                                                 <  1:75770/250‑1 (MQ=255)                                                                                      gcgcCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCcttctt                                                                                                                                                             <  2:587114/250‑1 (MQ=255)                                                                                        tcaaaCGTCATTCTGCCATTCGCCATTTTTAATGGTTTCCGCATCAGGGTAGAGTGCTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGGTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATACGGACGCAACAGGAATTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATCTGCCGGAATAGCCAGGCTGTCCATCCAGAAACTGACGCCTTCTTTCg                                                                                                                                                          >  2:568778/4‑251 (MQ=255)                                                                                        gcCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCg                                                                                                                                                          >  1:275373/1‑251 (MQ=255)                                                                                                              ccATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGt                                                                                                                                    >  1:131299/1‑251 (MQ=255)                                                                                                                              cAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCa                                                                                                                    <  1:463232/251‑1 (MQ=255)                                                                                                                                                     tCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATACGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTcc                                                                                                 >  1:592351/1‑247 (MQ=255)                                                                                                                                                      cGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGAGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTcc                                                                                                 >  1:493698/1‑246 (MQ=255)                                                                                                                                                             cACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCg                                                                                      >  1:321934/1‑250 (MQ=255)                                                                                                                                                                   tggcctgaacatctgaCGCCCCGCAAGGTTTGGGGTGGGATAACCGTTAGTTTCAGAACCCTGTTTGGCCACATCCGGGCGCAACATGTATTTGATCAATTGCAGCTCGTCATCTTTGGTGTGGGCATTTTCCGGGATCGCCTGGCTTCCCTTCCAGAAAATGCCGTTTTCTTTCTGCCACATCTCGGCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAATCATGCCAGCTCATGccttggtta                                                                                <  2:567550/235‑8 (MQ=255)                                                                                                                                                                        ttAACCGCTTACGCGCCGCAAGGTTTGGCTTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGAGCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTTCAGATCATGCCGAGGTTAACtt                                                                            <  2:392534/249‑1 (MQ=255)                                                                                                                                                                                          cAAGGTTTGGCTTTGGATAACCGATAGTTTCAGCATCCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCCGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTc                                                        <  2:481126/251‑1 (MQ=255)                                                                                                                                                                                                 tgacGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTAGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGACACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCGATGCACGGGTTCGCCGGGt                                                 >  2:465424/4‑251 (MQ=255)                                                                                                                                                                                                  ggCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTTTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGGTAACTTCGCCTTCCATGTACGGGGTCGCCGGGtt                                                <  1:180332/251‑1 (MQ=255)                                                                                                                                                                                                       tGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCgg                                           >  1:140833/1‑251 (MQ=255)                                                                                                                                                                                                            aaCCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGtt                                       <  1:16132/250‑1 (MQ=255)                                                                                                                                                                                                                gATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAACAGGAAGATGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATACAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTAGCCTTCCATGTACGGGTTCGCCGGGGTATCGGAGTTCAAgg                                  >  1:258596/1‑251 (MQ=255)                                                                                                                                                                                                                             aCCTGTTTTGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTgg                     >  1:447754/1‑251 (MQ=255)                                                                                                                                                                                                                                    ttGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAg               <  2:571755/250‑1 (MQ=255)                                                                                                                                                                                                                                    ttGCCACATCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAGt              >  1:578328/1‑251 (MQ=255)                                                                                                                                                                                                                                          caTCCGGGCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAGTTTTTTc        >  1:421957/1‑251 (MQ=255)                                                                                                                                                                                                                                                ggCGCACCAGGAAGTTGATCAATTCCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGACCGCCAGGCTGTCAATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAGTTTTTTCAGCTCg  <  2:442861/251‑1 (MQ=255)                                                                                                                                                                                                                                                ggCGCAACAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAGTTTTTTCAGCTCg  >  2:176090/1‑251 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                     AACGGGCGGTAATACCACCGCCCGCTTGCTGAATTAACGTCCTGCTTTCAGCTTCTGATAATACTCTTCATAAATGCTGCTGGCTGCGCCAACGTCATTCTGCCATTCGCCATTTTTAATGGTTTCAGCATCCGGGTAGAGTGTTTTATCGTTCGCCACTTCTGGACTTAACAGCTTACGCGCCGCAAGGTTTGGCGTTGGATAACCGATAGTTTCAGCAACCTGTTTTGCCACATCCGGGCGCAGCAGGAAGTTGATCAATTTCAGCGCGCCTTCTTTGTTTTTGGCATTTGCCGGGATCGCCAGGCTGTCCATCCAGAAAATGCCGCCTTCTTTCGGCCACACCACGTCAATTGGCGTACCCGCCTGGCGTGCAACGAAAGCAGAACCGTTCCAGATCATGCCGAGGTTAACTTCGCCTTCCATGTACGGGTTCGCCGGGTTATCGGAGTTAAAGGCTGCCACGTTTGGCATCAGTTTTTTCAGCTCG  >  NC_000913/1181750‑1182239

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑