Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,928,970	T→A	8.7%	K401M (AAG→ATG)	cheA ←	chemotaxis histidine kinase CheA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,928,970	0	T	A	8.7%	127.1 / 2.8	48	K401M (AAG→ATG)	cheA	chemotaxis histidine kinase CheA
Reads supporting (aligned to +/- strand):  ref base T (19/24);  new base A (2/2);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.76e-01

CAGATTGATCTCTTTCTTCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTGGCGGCGT  >  NC_002947/4928825‑4929111                                                                                                                                                   |                                                                                                                                              cAGATTGATCTCTTTCTTCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTg                                                                                                                                             <  6:125997/148‑1 (MQ=255)       gATCTCTTTCTTCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATg                                                                                                                                       <  4:105132/148‑1 (MQ=255)       gATCTCTTTCTTCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCATgtccaagg                                                                                                                                      >  2:200258/1‑142 (MQ=255)             tttcttCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCtc                                                                                                                                  <  8:192425/147‑1 (MQ=255)             tttcttCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCATGTCCAAGGccgtg                                                                                                                                 >  8:110204/1‑145 (MQ=255)               tcttcAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCtcgtcg                                                                                                                              >  7:266050/1‑149 (MQ=255)               tcttcAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCATGTCCAAGGccgtg                                                                                                                                 <  7:110204/146‑4 (MQ=255)               tcttcAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCATGTCCAAGGccgt                                                                                                                                  <  1:200258/145‑3 (MQ=255)                    aGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCt                                                                                                                         >  7:5324/1‑149 (MQ=255)                         gcgcgcCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCa                                                                                                                    <  6:183253/149‑1 (MQ=255)                           gcgcCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAgg                                                                                                                  <  4:102599/149‑1 (MQ=255)                           gcgcCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACAAGGCCTCGTCGCCGCTGTTCAgg                                                                                                                  <  7:209697/149‑1 (MQ=255)                                   tCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGgcg                                                                                                          >  7:258960/1‑149 (MQ=255)                                     gcgAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGGTTTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGgcg                                                                                                          >  1:263033/1‑148 (MQ=255)                                     gcgAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCa                                                                                                        >  1:289331/1‑149 (MQ=255)                                      cgAACCAGGCGCGGGAAGCGGCCGAAGACCTTCATGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCAc                                                                                                       <  7:106085/149‑1 (MQ=255)                                                gcgGGAAGCGGCCGAAGACCTTCTTGATCTGCTGCATACGTG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTa                                                                                             <  5:248731/149‑1 (MQ=255)                                                  gggAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACg                                                                                           <  2:263033/149‑1 (MQ=255)                                                     aaGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACgcac                                                                                        <  1:216419/149‑1 (MQ=255)                                                      aGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACgcacc                                                                                       <  4:322448/149‑1 (MQ=255)                                                           ccGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACgcaccagcac                                                                                  <  1:2164/149‑1 (MQ=255)                                                           ccGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACgcaccagcac                                                                                  <  8:5324/149‑1 (MQ=255)                                                             gAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACgcaccagcacca                                                                                <  5:300744/149‑1 (MQ=255)                                                              aaGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCg                                                                                                 >  6:269951/1‑131 (MQ=255)                                                              aaGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCg                                                                                                 <  5:269951/131‑1 (MQ=255)                                                                 aCCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTc                                                                            <  8:266050/149‑1 (MQ=255)                                                                   cttcttGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGc                                                                          >  3:316219/1‑149 (MQ=255)                                                                    ttcttGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGcc                                                                         >  2:24098/1‑149 (MQ=255)                                                                           tCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGACAAGGTTGGACACGGCCGTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATg                                                                  <  1:277494/149‑1 (MQ=255)                                                                               cTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCa                                                              <  1:24098/149‑1 (MQ=255)                                                                               cTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTACAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCa                                                              >  8:111206/1‑149 (MQ=255)                                                                                tGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCAt                                                             <  4:316219/149‑1 (MQ=255)                                                                                   aTACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCCGGCCCAGGCGCCCCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCAGGAt                                                          >  8:175552/1‑149 (MQ=255)                                                                                      cGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGAtctc                                                       >  3:176454/1‑149 (MQ=255)                                                                                         g‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTc                                                    <  5:99058/149‑1 (MQ=255)                                                                                                atcaCCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGgcg                                              >  3:256850/1‑149 (MQ=255)                                                                                                 tcaCCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGgcgc                                             >  1:120886/1‑149 (MQ=255)                                                                                                   aCCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTCGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGTCCCAGGCGCACCAGGCGGTAAAGCACCAGCACCACTTCGCCGACCATGTTCATGATCACGTCCATgcgagc                                           >  8:292543/1‑149 (MQ=255)                                                                                                        ggTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGgtgt                                      <  8:258960/149‑1 (MQ=255)                                                                                                          tCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTc                                     >  5:199781/1‑148 (MQ=255)                                                                                                               aGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGAcgcg                               >  4:158785/1‑149 (MQ=255)                                                                                                                      cggTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACggtg                        <  4:256850/149‑1 (MQ=255)                                                                                                                                gTCAAGGTTGGACACGGACTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCAAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCtt              >  4:58570/1‑149 (MQ=255)                                                                                                                                      gTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTgg        >  7:90218/1‑149 (MQ=255)                                                                                                                                         ggACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTggcgg     >  6:124901/1‑149 (MQ=255)                                                                                                                                          gACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTggcgg     <  8:90218/148‑1 (MQ=255)                                                                                                                                          gACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTggcgg     <  2:289331/148‑1 (MQ=255)                                                                                                                                            cacGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTGGCGGCGt  <  7:8739/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                              CAGATTGATCTCTTTCTTCAGCTGGCGCGCCAGGTCGCGAACCAGGCGCGGGAAGCGGCCGAAGACCTTCTTGATCGGCTGCATACGGG‑TTTTCATCACCGCGGTCTGCAGGTCGGCGGTGACCACGTCAAGGTTGGACACGGCCTTGGACATGGCCTCGTCGCCGCTGTTCAGGCCCAGGCGCACCAGGCGGTTACGCACCAGCACCAGTTCGCCGACCATGTTCATGATCTCGTCCAGGCGCGCGGTGTCGACGCGCACGGTGGTTTCCGCTTCGCTGGCGGCGT  >  NC_002947/4928825‑4929111

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑