Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,346,861	C→T	A95V (GCT→GTT)	ptsN →	phosphotransferase system enzyme IIA(Ntr)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,346,861	0	C	T	96.7%	87.3 / ‑6.1	30	A95V (GCT→GTT)	ptsN	phosphotransferase system enzyme IIA(Ntr)
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (13/16);  minor base G (1/0);  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 = 9.98e-01

GTTCTTAACAGGGAATGTACGCGAAGCCGCGTCCACTGTCAGAGCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGCTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGA  >  NC_000913/3346614‑3347106                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      gtTCTTAACAGGGAATGTACGCGAAGCCGCGTCCACTGTCAGAGCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGtttt                                                                                                                                                                                                                                                    >  1:103522/1‑251 (MQ=255)        aCAGGGAATGTACGCGAAGCCGCGTCCACTGTCAGAGCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCGGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGTCTATAGTTTTCGATGcc                                                                                                                                                                                                                                             <  2:384599/251‑1 (MQ=255)                        aaGCCGCGTCCACTGTCAGAGCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCgg                                                                                                                                                                                                                             >  1:227758/1‑251 (MQ=255)                           ccGCGTCCACTGTCAGAGCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTgg                                                                                                                                                                                                                          >  2:330810/1‑251 (MQ=255)                                    cggtcaaagaaaaaaaCGCGCCCTGGAAATCATAAGCGAGCTGGCGGGGAAACAACTTAGCCGGCCGCCTCAGGTGGTTTTTGAAGTTATCCTGACGCGG‑AAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACtttt                                                                                                                                                                                                                <  2:146816/241‑1 (MQ=255)                                            gCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCctg                                                                                                                                                                                                         <  1:130090/251‑1 (MQ=255)                                                        cccTGGAAAACATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCa                                                                                                                                                                                             <  2:80065/251‑1 (MQ=255)                                                              aaaTCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCa                                                                                                                                                                                        >  1:40864/1‑250 (MQ=255)                                                                          aGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCAc                                                                                                                                                                           >  2:112795/1‑251 (MQ=255)                                                                           gCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCAcc                                                                                                                                                                          >  2:128583/1‑251 (MQ=255)                                                                                      aacaacTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTTCCGGCAGACCAAACTAAAACGCACCTGCATACTCTg                                                                                                                                                               <  1:121427/251‑1 (MQ=255)                                                                                              aGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACTCGGGAAAAAATGGGCAGTACCGTTATCGGCAATGGTATGGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGTGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCtgg                                                                                                                                                        <  2:335494/250‑1 (MQ=255)                                                                                                 cggccgctTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGGACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGc                                                                                                                                                    <  2:229248/249‑1 (MQ=255)                                                                                                   gccgccTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCg                                                                                                                                                   <  1:253932/250‑1 (MQ=255)                                                                                                      gccTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAAc                                                                                                                                               >  2:211839/1‑251 (MQ=255)                                                                                                                       aaGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGAATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCATATAGGCTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTAGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGCCGAAACGTCTGGCGGACAAAAcc                                                                                                                              >  1:264027/1‑251 (MQ=255)                                                                                                                                                     gTACCGGTATCGGCAATGGAATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGc                                                                                                >  2:155530/1‑251 (MQ=255)                                                                                                                                                               cGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCTGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAagag                                                                                       <  1:59644/250‑1 (MQ=255)                                                                                                                                                                              cATTCCGCATGGCAAACTGGAAGAAGATGATCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTa                                                                       <  2:87252/251‑1 (MQ=255)                                                                                                                                                                                    gCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATa                                                                 <  1:309779/251‑1 (MQ=255)                                                                                                                                                                                     cATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTATCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATAc                                                                >  2:225800/1‑251 (MQ=255)                                                                                                                                                                                      aTGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAGCCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAGACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGANAcc                                                               >  2:373262/1‑251 (MQ=255)                                                                                                                                                                                         gCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTGCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACATCCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAAGCATTACGGATACCGaa                                                            <  1:289033/251‑1 (MQ=255)                                                                                                                                                                                                      agaTACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATg                                               >  2:59553/1‑251 (MQ=255)                                                                                                                                                                                                        aTACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGa                                              >  1:26205/1‑250 (MQ=255)                                                                                                                                                                                                          aCTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCTTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAg                                            <  2:161001/250‑1 (MQ=255)                                                                                                                                                                                                               gcgcgcCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGt                                      <  1:128583/251‑1 (MQ=255)                                                                                                                                                                                                                   gcCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTAtt                                  <  2:407542/251‑1 (MQ=255)                                                                                                                                                                                                                    ccGTTGGCGTGTTCGTTAAGCTCGAAACGCTTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCCCCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTc                                 <  2:220737/251‑1 (MQ=255)                                                                                                                                                                                                                                                  cTATAGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGCAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTgagg     >  2:221235/1‑249 (MQ=255)                                                                                                                                                                                                                                                    ataGTTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGgaga  >  1:287644/1‑250 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                      GTTCTTAACAGGGAATGTACGCGAAGCCGCGTCCACTGTCAGAGCAAAAAACGCGCCCTGGAAATCATCAGCGAGCTGGCGGCGAAACAACTTAGCCTGCCGCCTCAGGTGGTTTTTGAAGCTATCCTGACGCGGGAAAAAATGGGCAGTACCGGTATCGGCAATGGTATTGCCATTCCGCATGGCAAACTGGAAGAAGATACTCTGCGCGCCGTTGGCGTTTTCGTTCAGCTCGAAACGCCTATAGCTTTCGATGCCATCGACAACCAACCGGTGGACTTACTTTTTGCCCTGCTGGTGCCGGCAGACCAAACTAAAACGCACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGA  >  NC_000913/3346614‑3347106

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑