Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,461,707	C→A	8.4%	P236T (CCG→ACG)	lolC →	lipoprotein releasing system transmembrane protein LolC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,461,707	0	C	A	8.4%	152.0 / 4.1	51	P236T (CCG→ACG)	lolC	lipoprotein releasing system transmembrane protein LolC
Reads supporting (aligned to +/- strand):  ref base C (22/24);  new base A (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01

ACCGTGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTTGCTGCTGATCGTGGCGGT  >  NC_002947/2461560‑2461852                                                                                                                                                    |                                                                                                                                                    aCCGTGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGgcgc                                                                                                                                                     <  1:131134/148‑1 (MQ=255)  ccGTGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGcgccg                                                                                                                                                   >  3:74770/1‑149 (MQ=255)   cGTGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGCCCTGTTCCAGGcgccgc                                                                                                                                                  >  3:172436/1‑149 (MQ=255)   cGTGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGcgccgc                                                                                                                                                  >  7:93220/1‑149 (MQ=255)     tGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCcgcgc                                                                                                                                                <  7:116966/149‑1 (MQ=255)        ttGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCcgcgcg                                                                                                                                               >  1:136693/1‑147 (MQ=255)               cTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGa                                                                                                                                      <  1:171644/149‑1 (MQ=255)                ttCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑g                                                                                                                                    >  4:271410/1‑149 (MQ=255)                  ccACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCTACGCGCGGCGCCTGGaa                                                                                                                                     <  2:54904/147‑2 (MQ=255)                                 ggAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTgg                                                                                                                  <  3:123208/149‑1 (MQ=255)                                      tCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCTGCTGGGCGat                                                                                                             <  3:271410/149‑2 (MQ=255)                                      tCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGAc                                                                                                             <  8:93220/149‑1 (MQ=255)                                           ggCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAgg                                                                                                         >  5:163300/1‑148 (MQ=255)                                           ggCTACCTGGGCCTGACCAACATAAGCGACCTGTCACGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGcc                                                                                                                             >  2:186496/1‑129 (MQ=255)                                             cTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGACGCATCGCCCA‑GCAGCTGGGCGACCAGGaa                                                                                                       <  1:23407/149‑1 (MQ=255)                                                          aCCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGa                                                                                         >  8:67371/1‑149 (MQ=255)                                                            cAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCtata                                                                                                >  8:191055/1‑140 (MQ=255)                                                            cAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCtata                                                                                                <  7:191055/140‑1 (MQ=255)                                                            cAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACt                                                                                       >  3:232297/1‑149 (MQ=255)                                                              aCATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTg                                                                                      >  2:14977/1‑148 (MQ=255)                                                                      gACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTAc                                                                             <  4:232297/149‑1 (MQ=255)                                                                        ccTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTAccc                                                                           >  2:132101/1‑149 (MQ=255)                                                                         cTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTa                                                                              >  7:17458/1‑145 (MQ=255)                                                                         cTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTa                                                                              <  8:17458/145‑1 (MQ=255)                                                                          tGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAg                                                                                                          >  3:254988/1‑116 (MQ=255)                                                                          tGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAg                                                                                                          <  4:254988/116‑1 (MQ=255)                                                                            tCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAg                                                                                               >  4:162932/1‑125 (MQ=255)                                                                            tCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAg                                                                                               <  3:162932/125‑1 (MQ=255)                                                                            tCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACgg                                                                       >  7:20144/1‑149 (MQ=255)                                                                                  cTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCt                                                                 <  7:67371/149‑1 (MQ=255)                                                                                     cACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTa                                                              <  6:163300/149‑1 (MQ=255)                                                                                     cACCGCTGGAAGCCAGACCAGGTGCAGGGCCTGCGCCTGAAGTTCGACGACCTTTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTa                                                              <  5:157242/149‑1 (MQ=255)                                                                                        cGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTg                                                                >  8:137351/1‑144 (MQ=255)                                                                                        cGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTg                                                                <  7:137351/144‑1 (MQ=255)                                                                                        cGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCa                                                           <  4:172436/149‑1 (MQ=255)                                                                                          cTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAgg                                                         <  1:14977/149‑1 (MQ=255)                                                                                             gAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGa                                                      >  6:212400/1‑149 (MQ=255)                                                                                              aaGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGAt                                                     <  3:48944/149‑1 (MQ=255)                                                                                                gCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGTCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATcc                                                   >  1:241117/1‑149 (MQ=255)                                                                                                    gACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCTGTACCCACGGCAACCTGTACCAGGCGATCCGTAt                                               <  4:74770/149‑1 (MQ=255)                                                                                                     aCCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATg                                              >  3:298590/1‑149 (MQ=255)                                                                                                       cAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATgg                                             >  7:268153/1‑148 (MQ=255)                                                                                                        aGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGATTTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGa                                            >  6:316869/1‑148 (MQ=255)                                                                                                        aGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGa                                            >  3:126724/1‑148 (MQ=255)                                                                                                         ggTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAAtt                                                                                                     >  7:89556/1‑90 (MQ=255)                                                                                                         ggTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAAtt                                                                                                     <  8:89556/90‑1 (MQ=255)                                                                                                                    tGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACAAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCACGAt                                >  5:59549/1‑148 (MQ=255)                                                                                                                        ccTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCAGGCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGc                            >  1:82593/1‑149 (MQ=255)                                                                                                                                   acgacCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTtgctg                <  4:298590/149‑1 (MQ=255)                                                                                                                                   acgacCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTtgctg                <  4:126724/149‑1 (MQ=255)                                                                                                                                     gacCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTTgctgct              <  2:82593/149‑1 (MQ=255)                                                                                                                                       gatgctCCAGGCTACGCGCGGCGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTTGCTGCTGa            >  3:110372/6‑149 (MQ=255)                                                                                                                                           ctCCAGGCTACGCGCGGCGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAAc                                                                   <  7:74453/89‑1 (MQ=38)                                                                                                                                            tCCAGGCTACGCGCGGCGCCTGGA‑GCATCGCACA‑GCAGCTGGCCGACCAGGAATTCTATAGCCGTGACTGGACCCCTACCCACGGCAACCAGTACAACGCGATACCTATGGAAAAGGCCATGATCGGCCGGCTGTTGCGGCTCAACgtt       >  6:87492/1‑148 (MQ=255)                                                                                                                                              cAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTTGCTGCTGATCgtgg      <  2:241117/148‑1 (MQ=255)                                                                                                                                                 gcgcCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTTGCTGCTGATCgtggcggt  >  2:248644/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                    ACCGTGGTTGGCACCTTCCACGTTGGCGCGGGGGAGATCGACGGCTACCTGGGCCTGACCAACATCAGCGACCTGTCCCGCCTGCACCGCTGGAAGCCCGACCAGGTCCAGGGCCTGCGCCTGAAGTTCGACGACCTGTTCCAGGCGCCGCGCGTAGCCTGGA‑GCATCGCCCA‑GCAGCTGGGCGACCAGGAATTCTATAGCCGTGACTGGACCCGTACCCACGGCAACCTGTACCAGGCGATCCGTATGGAAAAGGCCATGATCGGCCTGCTGTTGCTGCTGATCGTGGCGGT  >  NC_002947/2461560‑2461852

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: ‑