Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,637,898	G→C	T401A (ACG→GCC)	creC →	sensory histidine kinase CreC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,637,898	0	G	C	96.9%	84.6 / ‑3.5	32	T401A (ACG→GCC)	creC	sensory histidine kinase CreC
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base C (11/20);  total (11/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.06e-01

TGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAGCGCCGAAGTGGATCAGGAACACGTCACGCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTTTCACGTATTTTTGAACGCTTTTACTCTTTGCCTCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCAC  >  NC_000913/4637669‑4638137                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                tGACTGTTGTTGATGTGGCGGCATTATTTCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAACATCACTCTACATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGt                                                                                                                                                                                                                            >  1:202727/1‑251 (MQ=255)                    ggcATTATTTCGCCGCGGCAGCGAATCGATCACCGTGCAGTTGGCAGAAAAAAATATCCCTTTACATGTTATGCCCTCTGAGGTTAATTTTGATGCTGAACCGGCTTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCTCCCTTAAGGTGCTGTAGACCGGTAGTGGTATTCCTGACTAcg                                                                                                                                                                                                         <  2:63590/251‑1 (MQ=255)                              cgccgcGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAACATCACTCTACATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACg                                                                                                                                                                                               <  1:248712/251‑1 (MQ=255)                                ctgcgTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAACATCACTCTACATGTTATGCCTACCGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCTCTGGGGAATTTACTGGATAACGCCAGCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTTACTACGCGCTGTCACg                                                                                                                                                                                               <  2:37153/247‑1 (MQ=255)                                        gCGAAGCGCGCACCGTGCAGTTTGCAGAAAAAAACATCACTCTACATGTTATGCCCACTGAGGGTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGATGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGaa                                                                                                                                                                                     <  2:104248/251‑1 (MQ=255)                                          gAAGCGCGCACCGTGCAGTTGGCAGAAAAAAACATCACTCTACATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATGCCGGTAGAGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACg                                                                                                                                                                                   >  1:263088/1‑251 (MQ=255)                                          gAAGCGCGCACCGTGCAGTTGGCAGAAAAAAACATCACTCTACATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACg                                                                                                                                                                                   >  1:371013/1‑251 (MQ=255)                                              cgcgcACCGTGCAGTTGGCAGAAAAAAAAATCAATCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAGCGCCGAAGTGGATCAGGAACACGTCACGCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTTTCACGTATTTTTGAACGCttt                                                                                                                                                                               <  1:59037/251‑1 (MQ=255)                                               gcgcTCCGGGCAGTTGGCTGAAAAAAGCATCACGCGACATGTTATGCCCGCTGAGGTTAATGTGGCTGCTGACCCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCtttt                                                                                                                                                                              <  2:114885/251‑1 (MQ=255)                                                                   aaaaaaacaTCACTCTACATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCTGTCGCATAACTCTAAGCGCCGAAGTGGATCATGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAAt                                                                                                                                                          <  1:240021/251‑1 (MQ=255)                                                                      aaaaaaTCACTCTACATGTTATGCCCACTGAGGTTAATTTTGCTGCTGAACCGTCGTTACTTGAGCAGGCTCTGTGGAATTTACTTGATAACGCCATCGATTTTACCCCCGAGAGCGTTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAATGTGCTGGATACCGGTAGTGGTATTCCTGACTACTCGCTGTCACATATTTTTGAACGCTTTTACTCTTTGCCGCATGCAAATggg                                                                                                                                                       <  2:173717/251‑1 (MQ=255)                                                                       aaacaTCACTCTACATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCACATGGGc                                                                                                                                                      >  1:143313/5‑251 (MQ=255)                                                                                tctacATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAagc                                                                                                                                              >  1:4952/5‑250 (MQ=255)                                                                                   acATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCg                                                                                                                                          <  1:159609/250‑1 (MQ=255)                                                                                   acATGTTATGCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCg                                                                                                                                          >  1:151729/2‑251 (MQ=255)                                                                                    cATGTTATTCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGGTACTGGAGCAGGCGCTGGGGAATTTACTGGAGAACGCCATCGATTTTACCCCCGAGAGCGGTCGCAGAACGCTAAGCGCCGAAGTGTATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTGTGAACGCTTTTACGCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCg                                                                                                                                          <  2:236118/250‑1 (MQ=255)                                                                                          atgCCCACTGAGGTTAATGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTgg                                                                                                                                    <  1:93393/248‑1 (MQ=255)                                                                                                               gctgctGACCCGGCGTTATTGTCGCAGGCGCTGGGGAATTTACTGGCTAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCGAAGCGCCGAAGTGGATCCGGAACACGTCGCCCTTAAGGTGTTGGATTCCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAATCTGCCGTCTGGGGTTGGCGTTCGGCAGTGAGGt                                                                                                              <  2:276643/251‑1 (MQ=255)                                                                                                                 gtcggAACCGTCGTTACTGGAGCAGGCGCTTGGGAATTTTCTGTATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATAACGCTAAGTGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCTCTGTCACGTATTTTTGAATGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTc                                                                                                             <  2:186163/246‑1 (MQ=255)                                                                                                                  gctgAACCGGCGTTACTGGAGCAGGCGCTGGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGc                                                                                                           <  1:195276/251‑1 (MQ=255)                                                                                                                   cagAACCGGCGTTACTGGAGCAGGCGCGGGGGAATTTACTGTAGAACTCCTTCCATTTTCCCCCCTAGAGCGGGCGCAGAACGCTAAGCGACGAAGTGGACGAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCGGTCACGTATTTTTGAACGCTTGTACTCTTTGCCGCGTGCATGTGGTCAAAAAAGCATCGTTCTGGGGGTGGCGTTCGTCAGTGTGGTCgac                                                                                                          <  2:249851/249‑3 (MQ=255)                                                                                                                     gAACCGGCGTTACGGGAGCGGGCGCTTGGGAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCGGTCACGGATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATTGGCAAAAAAGCAGCTGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCg                                                                                                        <  2:179516/251‑1 (MQ=255)                                                                                                                                                  gaaTTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTgcgc                                                                            >  1:346976/2‑250 (MQ=255)                                                                                                                                                       tACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTg                                                                      >  1:10534/1‑251 (MQ=255)                                                                                                                                                                 cGCCATCGATTTTACCCCCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTg                                                            <  1:301558/251‑1 (MQ=255)                                                                                                                                                                            atACCACCGAGAGCGGTCGCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGACGCCCTTAAGGTGCGGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTAATTTTGAACGCTTGTACTCTTTTCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGTGTTCGTCAGTGAGGTCGGCCGTTTGTTGAACGGCGAAGTCAAGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGc                                                  <  2:188819/249‑1 (MQ=255)                                                                                                                                                                                  ccgagagcgaacgcatagcGCTAAGCGCCGAAGTGGATCAGGAACACGACGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTAACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGAAAAAAAGCGGCGGTCTGGGGTTGTCGTTCGTCAGTGGGGTCGCCCGTTTGTTTAACGTGGAAGTCACGCTGCGCATAGTGCAGGAAGGTGGCGTGCTGGctccactt                                           >  2:69904/19‑244 (MQ=255)                                                                                                                                                                                              gCATAACGCTAAGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGt                               >  1:108942/1‑251 (MQ=255)                                                                                                                                                                                                        aaGCGCCGAAGTGGATCAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACAt                     <  1:11672/251‑1 (MQ=255)                                                                                                                                                                                                                        cAGGAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGTTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTcc     <  1:199855/251‑1 (MQ=255)                                                                                                                                                                                                                           gAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTTTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCATCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCcac  >  1:20854/1‑251 (MQ=255)                                                                                                                                                                                                                           gAACACGTCGCCCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTGTCACGTATTCTTGAACGCTTTTACTCTTTGCCGCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAACTCTTCCcac  <  1:374439/251‑1 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                TGACTGCTGTTGATGTGGCGGCATTATTCCGCCGCGTCAGCGAAGCGCGCACCGTGCAGTTGGCAGAAAAAAAAATCACTCTGCATGTTACGCCCACCGAGGTTAACGTTGCTGCTGAACCGGCGTTACTGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCTAAGCGCCGAAGTGGATCAGGAACACGTCACGCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTACGCGCTTTCACGTATTTTTGAACGCTTTTACTCTTTGCCTCGTGCAAATGGGCAAAAAAGCAGCGGTCTGGGGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGGTGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCAC  >  NC_000913/4637669‑4638137

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑