Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,165	A→C	12.1%	intergenic (‑129/‑139)	PP_5175 ← / → PP_5176	HlyD family secretion protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,903,165	0	A	C	12.1%	98.8 / 5.9	50	intergenic (‑129/‑139)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (19/24);  new base C (4/2);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.76e-01

AGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAC  >  NC_002947/5903017‑5903310                                                                                                                                                      |                                                                                                                                                  aGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                   <  1:180624/149‑1 (MQ=255) aGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                   <  1:45210/149‑1 (MQ=255) aGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                   <  2:220219/149‑1 (MQ=255)  gCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAg                                                                                                                                                  <  5:69436/149‑1 (MQ=255)   cGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCCGgcgcgc                                                                                                                                                 >  3:199694/1‑149 (MQ=255)   cGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGAAGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCACATAGCGGGCGAGc                                                                                                                                                 >  1:104122/1‑149 (MQ=255)       cGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcgc                                                                                                                                             <  5:137448/149‑1 (MQ=255)        gCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGCGCCcgc                                                                                                                                             >  3:119536/1‑148 (MQ=255)          atcatcGCCATGCTTGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGTGTGTGAGCGT‑AGTTTAGTGTTCGATAAACATCACTGACGGGGGACATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGGACGCGaa                                                                                                                                          <  2:110472/149‑1 (MQ=255)          aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTATTAGCGGGCGAGCCcgcg                                                                                                                                            >  1:324545/1‑148 (MQ=255)          aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGAGGCCTCTTCGCGGGCTCGCCCGCGaa                                                                                                                                          <  5:60261/149‑1 (MQ=255)              aCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAgg                                                                                                                                      >  8:320384/1‑149 (MQ=255)              aCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTAATAGCGGGCGCGCCCGCGAAGAgg                                                                                                                                      >  3:114328/1‑149 (MQ=255)               cGCCATGGTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGGATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGc                                                                                                                                     <  2:317860/149‑1 (MQ=255)                 ccATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTATTCGCGGGCGAGCCGCCGAAGAGGCCt                                                                                                                                   >  8:75770/1‑149 (MQ=255)                      cTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTTAGGTT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCcac                                                                                                                               <  6:345943/148‑1 (MQ=255)                         gagctttgcttgTGCAAAATTGTTTTGTGGTATGCGACTGGGTGCGT‑AGTGCTGGGGTCGAAAAACAGCACTTCCGGGGCCCATGCTGGCATTTTTGGGGCGTGCGGGGGCCTGTTCGCGGGCTAGCCCGCGAAGAGGCCTCCACAGcc                                                                                                                           <  4:147947/144‑1 (MQ=255)                         gCTCCTTGCTTGTGCAAAAATGTTTTGTGGGTTGCGACTGTGTGCGT‑AGTTCAGGTTTCTATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGGGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGcc                                                                                                                           <  4:119536/149‑1 (MQ=255)                           tCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcgc                                                                                                                                             >  7:175330/1‑129 (MQ=255)                           tCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGAGCCCGCGGAGATGCCTCCACAGCCAt                                                                                                                         >  5:226615/1‑149 (MQ=255)                              ttgcttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAag                                                                                                                                         >  3:27451/1‑130 (MQ=255)                              ttgcttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAag                                                                                                                                         <  4:27451/130‑1 (MQ=255)                                    gtgCACAATTTTTTTGTGGTATGCTACTGTGAGCTT‑AGTTCTGGGTTCTATAAACATCACTGCGGGGGGCCATGCTGGCATTTTTGGTGCCTGGGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGCCTCCACAGCCATGTATCa                                                                                                                   <  4:199694/146‑1 (MQ=255)                                       cacaAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcgc                                                                                                                                             <  5:258186/117‑1 (MQ=255)                                       cacaAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCcgc                                                                                                                                             >  6:258186/1‑117 (MQ=255)                                            aTGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGGGGGGCCGCGAAGAGGCCGCCCCAGCCCTGTTTGAGTAtgtggcc                                                                                                         >  3:52242/1‑145 (MQ=255)                                                     gggATGCGACTGTGAGCTT‑AGTTCTGGGTTCTATAAACTTCACTGACGGGGGCCTTGCTGGCTTTTTTGGTGCCTGGGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGaaa                                                                                               <  5:43777/149‑1 (MQ=255)                                                           cGACTGTGAGCGT‑AGTTCAGGGGTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCa                                                                                         <  7:320384/149‑1 (MQ=255)                                                                   aGCGT‑AGTTCAGGTTTCGATAAACATCACTGAGGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCg                                                                                  <  2:324545/148‑1 (MQ=255)                                                                      gT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAg                                                                                        <  5:310700/139‑1 (MQ=255)                                                                      gT‑AGTTCAGGGTTCGATAAACATCACTGACGGCGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTAATCGCGGGCGAGCCCGCGAAGACGCCACCACACCCATGTATCACTATCTGCCATATCCACAAACCAACAg                                                                                        >  6:310700/1‑139 (MQ=255)                                                                              aGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCg                                                                        <  7:75770/148‑1 (MQ=255)                                                                                      aTAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGa                                                                                                                                           <  6:279763/73‑1 (MQ=255)                                                                                      aTAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGa                                                                                                                                           >  5:279763/1‑73 (MQ=255)                                                                                       tAAACATCACTGCCGGGGGCCTTGCTGGCATTTTTGGGGCCGGGGGGGGCCGCTTCGCGGGCTAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAAc                                                                 <  4:52242/146‑1 (MQ=255)                                                                                       tAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTACACAGCCATGTATCAGTATCTGCCAGATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCgg                                                              >  1:56506/1‑148 (MQ=255)                                                                                               aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTAcc                                                          <  3:325356/145‑1 (MQ=255)                                                                                               aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCttt                                                       <  4:114328/148‑1 (MQ=255)                                                                                               aCTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTAATAGCGGGCGAGCCCGCGAAAAGGCCAACCCAGCCAAGTATAAATATATTCCAAAAACACAAAACAAAAGGCAAAGGCCAACCCCCATACAACCCCAAccaaa                                                       >  4:325356/1‑145 (MQ=255)                                                                                                          ccATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCt                                           <  4:34810/149‑1 (MQ=255)                                                                                                                                   gggggCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGcc                  <  3:161643/149‑1 (MQ=255)                                                                                                                                       gccgatgcgcgGCCGAGCCGGCCAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTa              <  4:219920/142‑1 (MQ=255)                                                                                                                                       gCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGt                >  2:35246/1‑147 (MQ=255)                                                                                                                                        ccTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCAGGAATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAAGCGCTACATTGAACAGGGAGGCTCACATTCac                                  >  7:366519/1‑127 (MQ=255)                                                                                                                                          tctTCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGa                            >  6:131603/1‑132 (MQ=255)                                                                                                                                          tctTCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGa                            <  5:131603/132‑1 (MQ=255)                                                                                                                                          tctTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGACACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc           >  7:191229/1‑149 (MQ=255)                                                                                                                                          tctTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAg                                 <  6:73306/127‑1 (MQ=255)                                                                                                                                          tctTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAg                                 >  5:73306/1‑127 (MQ=255)                                                                                                                                          tctTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc           >  3:198774/1‑149 (MQ=255)                                                                                                                                            ttCGCCGGCTCGCCCGCGAAGAGGCCCCCACAGGCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGGATCGGACATCCGCGTACCAACCGCTACCTTTCACAGGGAGGCTCTCATTCAAGGATGATCAAAATCCCGTTAGcgc          >  8:68990/1‑146 (MQ=255)                                                                                                                                             tCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGaa        >  3:7404/1‑149 (MQ=255)                                                                                                                                                  ggCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCa   >  6:341905/1‑149 (MQ=255)                                                                                                                                                   gCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAc  <  6:226615/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                  AGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGT‑AGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAC  >  NC_002947/5903017‑5903310

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑