Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,137,670	C→T	7.9%	intergenic (‑69/‑144)	PP_4522 ← / → PP_4523	LysR family transcriptional regulator/agmatinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,137,670	0	C	T	7.9%	146.3 / 2.2	52	intergenic (‑69/‑144)	PP_4522/PP_4523	LysR family transcriptional regulator/agmatinase
Reads supporting (aligned to +/- strand):  ref base C (23/24);  new base T (2/2);  total (26/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.52e-01

GTTGGCAAAGCCCTGGTGGCGCACCACGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACACAACAATCGACCGACTGAT  >  NC_002947/5137527‑5137815                                                                                                                                                |                                                                                                                                                  gTTGGCAAAGCCCTGGTGGCGCACCACGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGaa                                                                                                                                              <  8:323680/149‑1 (MQ=255)      cAAAGCCCTGGTGGCGCACCACGCTGATGAAGATGCGCAGCAGTTTCATGTCGGGCAAGGTCGAGGCCATGGTGCAAAGGTTACACAAGTGTATGTGCGCGCAGTCTAACTTGTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTaa                                                                                                                                          <  2:37496/148‑1 (MQ=255)      cAAAGACCTGGTGGCGCACCACGCTGATGAAGATGCGCAGCAGGTTCAGGTAGGGCAAGGTCGAGGCCATGGTGCAAAGGTTCCACAACGGTATGTTCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTGCTGaaat                                                                                                                                            >  1:37496/1‑144 (MQ=255)       aaaGCCCTGGTGGCGCACCACGCTGATGAAGATGCTCATCAGTTTCAGGTAGGGCAAGGGCGAGGCCATGGTGCAACGGTTCCACAAGGGTCTGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGGAATTTCTGAACTaaag                                                                                                                                        <  4:234989/149‑3 (MQ=255)                     gcACCACGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGc                                                                                                                           >  7:13536/1‑148 (MQ=255)                      caccacGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGa                                                                                                                         <  7:305318/149‑1 (MQ=255)                      caccacGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGa                                                                                                                         >  1:217161/1‑149 (MQ=255)                        ccacGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGAtt                                                                                                                       >  1:258833/1‑149 (MQ=255)                                  gaAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGAttcttc                                                                                                                   <  8:3542/143‑1 (MQ=255)                                  gaAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGAttcttc                                                                                                                   >  7:3542/1‑143 (MQ=255)                                   aaGATGCGCAGCAGTTTCAGTTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGgc                                                                                                             <  6:334679/148‑1 (MQ=255)                                           cagcagTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCtt                                                                                                     >  4:30475/1‑148 (MQ=255)                                                               aGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGt                                                                                <  2:217161/149‑1 (MQ=255)                                                                 gTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTcc                                                                              <  2:258833/149‑1 (MQ=255)                                                                   cGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCt                                                                            >  4:311266/1‑149 (MQ=255)                                                                      ggCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGcc                                                                         >  2:110331/1‑149 (MQ=255)                                                                      ggCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGcc                                                                         >  4:41680/1‑149 (MQ=255)                                                                               gCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCa                                                                 >  7:281356/1‑148 (MQ=255)                                                                               gCAACGGTTCCACAAGGGTATGTGCGCCCAGTCTAACTGCTCTACCCGCATTTAGTTCAGAAATTCCTGAACTAAGTATTTCTCGGTAGCGAttc                                                                                                                      >  2:219971/1‑95 (MQ=255)                                                                                 aaCGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCt                                                                            >  7:99400/1‑135 (MQ=255)                                                                                 aaCGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCt                                                                            <  8:99400/135‑1 (MQ=255)                                                                                     gTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACcaca                                                          <  8:281356/149‑1 (MQ=255)                                                                                      ttCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGaa                                                                                                                                              >  6:121049/1‑64 (MQ=255)                                                                                          acaAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGcc                                                                                       <  8:160781/115‑1 (MQ=255)                                                                                          acaAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGcc                                                                                       >  7:160781/1‑115 (MQ=255)                                                                                          acaAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGaa                                                                                    >  3:85463/1‑118 (MQ=255)                                                                                          acaAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTg                                                      >  7:145265/1‑148 (MQ=255)                                                                                           caAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGaa                                                    >  5:27937/1‑149 (MQ=255)                                                                                              gggTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATgg                                                 >  4:295169/1‑149 (MQ=255)                                                                                                 tATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTcc                                                                              <  2:204996/117‑1 (MQ=255)                                                                                                     tgCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAAc                                                              >  5:261678/1‑129 (MQ=255)                                                                                                     tgCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAAc                                                              <  6:261678/129‑1 (MQ=255)                                                                                                      gcgcgcAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCgcgg                                          <  3:295169/148‑1 (MQ=255)                                                                                                          gcAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGca                                     <  3:41680/149‑1 (MQ=255)                                                                                                                tAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCccgc                                                                      >  4:215626/1‑110 (MQ=255)                                                                                                                tAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCccgc                                                                      <  3:215626/110‑1 (MQ=255)                                                                                                                 aaCTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTc                              >  7:282678/1‑149 (MQ=255)                                                                                                                 aaCTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTc                              >  4:146290/1‑149 (MQ=255)                                                                                                                  aCTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGTTTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTc                              <  8:282678/148‑1 (MQ=255)                                                                                                                  aCTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGtt                               <  6:27937/147‑1 (MQ=255)                                                                                                                  aCTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTc                              <  8:13536/148‑1 (MQ=255)                                                                                                                      ctctACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGaa                           <  1:110331/147‑1 (MQ=255)                                                                                                                           cccGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGaacaaa                       <  3:30475/146‑1 (MQ=255)                                                                                                                           cccGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGaacaaa                       <  4:69959/146‑1 (MQ=255)                                                                                                                            ccGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGgcg                                               <  6:167600/121‑1 (MQ=255)                                                                                                                            ccGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGgcg                                               >  5:167600/1‑121 (MQ=255)                                                                                                                             cGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACacaa                  <  3:146290/149‑1 (MQ=255)                                                                                                                                  ttAGTTCAGGAATTTCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCCCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACacaa                  >  3:75672/1‑144 (MQ=255)                                                                                                                                  ttAGTTCAGGAATTTCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCCCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACacaa                  <  4:75672/144‑1 (MQ=255)                                                                                                                                  ttAGTTCAGGAATTTCTGAACAAAGTATTTGTCGGAAGCGATTCTTCCCCGGCGCTCGCTTGAGAAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATCGCGCGCGGCGGCACAGCTTCGATAAAACACAACAATc             >  6:52160/1‑149 (MQ=255)                                                                                                                                         aGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACACAACAATcgaccga       >  3:130535/1‑148 (MQ=255)                                                                                                                                             aTTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACACAACAATCGACCGACtgat  <  8:145265/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                  GTTGGCAAAGCCCTGGTGGCGCACCACGCTGATGAAGATGCGCAGCAGTTTCAGGTCGGGCAAGGTCGAGGCCATGGTGCAACGGTTCCACAAGGGTATGTGCGCGCAGTCTAACTGCTCTACCCGCCTTTAGTTCAGAAATTCCTGAACTAAGTATTTGTCGGTAGCGATTCTTCCCCGGCGCTCGCTTGAGCAGACTTGGCCGAAATGTCCCTGCCCGCCGGCAAACCACACGTGAATGGCGCGCGGCGGCACAGGTTCGAACAAACACAACAATCGACCGACTGAT  >  NC_002947/5137527‑5137815

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑