Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,857,454	A→C	39.7%	intergenic (‑131/+166)	recR ← / ← ybaB	recombination protein RecR/nucleoid‑associated broad specificity regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,857,454	0	A	C	39.7%	33.8 / 33.6	42	intergenic (‑131/+166)	recR/ybaB	recombination protein RecR/nucleoid‑associated broad specificity regulator
Reads supporting (aligned to +/- strand):  ref base A (19/6);  new base C (4/13);  total (23/19)
Fisher's exact test for biased strand distribution p-value = 1.38e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAGAGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAGCGGCG  >  NC_002947/4857305‑4857598                                                                                                                                                      |                                                                                                                                                 tGAGAGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGaa                                                                                                                                                  <  1:1113875/150‑1 (MQ=255) tGAGAGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGaa                                                                                                                                                  <  1:4948938/150‑1 (MQ=255)  gagaGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAag                                                                                                                                                 <  2:1699238/150‑1 (MQ=255)  gagaGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAag                                                                                                                                                 <  2:5118916/150‑1 (MQ=255)  gagaGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAag                                                                                                                                                 <  2:5118826/150‑1 (MQ=255)  gagaGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAag                                                                                                                                                 <  2:4148077/150‑1 (MQ=255)    gagGGCTGAAGCTCATGGGAAAGGCCTGACAATTCCATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAagca                                                                                                                                               <  2:2591872/150‑1 (MQ=255)    gagGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAagca                                                                                                                                               <  1:74484/150‑1 (MQ=255)    gagGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAagca                                                                                                                                               <  1:1601160/150‑1 (MQ=255)       ggCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAAGCAGcc                                                                                                                                            <  1:2474613/150‑1 (MQ=255)       ggCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAAGCAGcc                                                                                                                                            <  1:3980406/150‑1 (MQ=255)        gCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCTTCGCAGccc                                                                                                                                           <  1:765612/150‑1 (MQ=255)          tGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTGGCGAAAAGGCTGCGGAACAAccccc                                                                                                                                         >  1:608662/1‑149 (MQ=255)            aaGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAGGGGCTTCTTCGCAGccctttc                                                                                                                                       <  2:334912/150‑5 (MQ=39)            aaGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAGGGGCTGCTTCGCAGccctttc                                                                                                                                       <  2:334854/150‑5 (MQ=39)            aaGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCTTCGCAGccctttc                                                                                                                                       <  1:3622164/150‑5 (MQ=255)            aaGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCTTCGCAGccctttc                                                                                                                                       <  2:3733958/150‑5 (MQ=255)            aaGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCTTCGCAGccctttc                                                                                                                                       <  2:2439028/150‑5 (MQ=255)              gCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAGGGGCTGCTTCGCAGccctttcgc                                                                                                                                     <  2:2720036/150‑7 (MQ=39)              gCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAGGGGCTGCTTCGCAGccctttcgc                                                                                                                                     <  2:2720086/150‑7 (MQ=39)                    gtgAACGGCCTCACACTTCAATACGAGGCGGTTTATACCCAGGGGGGGCGGGGGCGTCAAACCACCGCGCCCAACGCCTGAAAGGTCTGCTTTTTTGGGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCTAAGCAGCCCCGGCACTCtgtg                                                                                                                               <  2:5127453/148‑1 (MQ=37)                                          aaGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCgggg                                                                                                         >  1:2522365/1‑150 (MQ=255)                                                     tataCCCCGGGGGGGGGGTGGCTACAAAAAACCCCCCCAAACGCCTGAATGGTTTGTTTTTTTGTGGGCGCGGCTTTTGGCCGCGACGGGGCTGCCCCGCCGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCgcgc                                                                                              <  1:2782006/150‑1 (MQ=255)                                                     tataCCCAGGGGGGGCGGTGGCGTAAAACCACCTCGCCCAACGCCTGCATGGTGTGCTTTTTTGGGGGCGCGGCCTTGTGGCGCTAATGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCgcgc                                                                                              <  2:325191/150‑1 (MQ=255)                                                       taCCCTGCGGGGGCGGTGGCGTAAAATCACCTCGCCCAACGCCTGCAAGGTCTGCTTTTTTGTGGGTGCGGCGTTGTGTCGCTAACGGGCTGCGACGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGccc                                                                                            <  2:1799819/150‑1 (MQ=255)                                                           cAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGccccggg                                                                                        >  1:1303922/1‑147 (MQ=255)                                                            cggggggggggTGGCGACAAATCACCTCGCCCAACGCCTGCACGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAATGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAGATCCCGGGGCCGCTTCGCGCCCCTTTc                                                                                       <  2:420865/147‑1 (MQ=37)                                                            aggggggggggTGGCTAAAAAACACCCCGCCCAACGCCTGCATGGTCTGCTTTTTTGTGGGCGCGGCCTTGTGCCGCTAAGGGGCTGGGACGCACCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGccccggga                                                                                       <  2:1303922/147‑5 (MQ=255)                                                              ggggggcgggggcGCAAAACCACCCCCCCCACCGCCTGCACGGTCTGTTTTTTGGGGGGCGCGGCGTTGTGGCGCTAACGGGCTGCGACCCCCCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTcgc                                                                                     <  2:1966272/149‑1 (MQ=255)                                                                       tGGCGTCAAACCCCCGCGCCCAACGCCTGCAGGGTCTGCTTTTTTGGGGGAGCGGCCTTGTGGCGCTAACGGGCTGCCACGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAgg                                                                            <  2:608662/150‑1 (MQ=37)                                                                                                                                ttGTGTCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGc                   >  1:5622894/1‑150 (MQ=255)                                                                                                                                    gtCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACt               >  1:5439551/1‑150 (MQ=255)                                                                                                                                     tCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtg              >  1:3108128/1‑150 (MQ=255)                                                                                                                                        tgccggggCTGCTTCGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtgttg           >  2:3404644/6‑150 (MQ=255)                                                                                                                                        cgAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtgttg           >  2:3163961/1‑150 (MQ=255)                                                                                                                                         gAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtgttgt          >  2:2089526/1‑150 (MQ=255)                                                                                                                                         gAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtgttgt          >  2:2089636/1‑150 (MQ=255)                                                                                                                                         gAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtgttgt          >  2:1368733/1‑150 (MQ=255)                                                                                                                                         gAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACtgttgt          >  1:4321191/1‑150 (MQ=255)                                                                                                                                            ggggCTGCTTCGCAGCCCTGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTctg       >  2:4754683/2‑148 (MQ=38)                                                                                                                                            ggggCTGCTTCGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAg       >  1:5527657/2‑150 (MQ=255)                                                                                                                                            ggggCTGCTTCGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAg       >  2:5249281/2‑150 (MQ=255)                                                                                                                                                cTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggc   >  1:4079555/1‑150 (MQ=255)                                                                                                                                                 tGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggcg  >  2:2970828/1‑150 (MQ=255)                                                                                                                                                 tGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggcg  >  1:2661808/1‑150 (MQ=255)                                                                                                                                                 tGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggcg  >  2:3382932/1‑150 (MQ=255)                                                                                                                                                 tGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggcg  >  1:1104430/1‑150 (MQ=255)                                                                                                                                                 tGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggcg  >  2:1146195/1‑150 (MQ=255)                                                                                                                                                 tGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAgcggcg  >  1:3362349/1‑150 (MQ=255)                                                                                                                                                   cGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACaaaa                                                              >  2:2713557/1‑88 (MQ=255)                                                                                                                                                   cGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACaaaa                                                              <  1:2713557/88‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                 TGAGAGGGCTGAAGCTCATGGGAAAGGCCTGACAATTCAATAAGAGGCGGTTTATACCCAGCGGGGGCGGTGGCGTCAAATCACCTCGCCCAAAGCCTGCAAGGTCTGCTTTTTTGTGGGAGCGGCCTTGTGTCGCGAAAGGGCTGCGAAGCAGCCCCGGCACTCTGTGCTGCGAAGCTGAAATCCCGGGGCCGCTTCGCGCCCCTTTCGCGACACAAGGCCGCTCCCACAAAAAAGCAGACCGCAACTGGGTTGAAATCTCCGCAAAAAAAACCGCCACTGTTGTCAGCGGCG  >  NC_002947/4857305‑4857598

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑