Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,941,121:1	+A	7.7%	coding (123/531 nt)	PP_3475 ←	type II secretion system pseudopilin PulG‑like signal peptide protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,941,121	1	.	A	7.7%	197.6 / 11.1	52	coding (123/531 nt)	PP_3475	type II secretion system pseudopilin PulG‑like signal peptide protein
Reads supporting (aligned to +/- strand):  ref base . (22/26);  new base A (2/2);  total (24/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-01

TTGGCCTGCGGGTAGCGGTTGTCCTGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGCCCTCCCTGTGGCACCGCTCTTGA  >  NC_002947/3940972‑3941270                                                                                                                                                       |                                                                                                                                                      ttGGCCTGCGGGTAGCGGTTGTCCTGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGggcg                                                                                                                                                        <  1:763948/150‑1 (MQ=255)                 ggTTGTCCTGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCACCCCTGGCGAGGCGCGGTAGTAGCTACGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCg                                                                                                                                       >  1:431073/1‑150 (MQ=255)                    tGTCCTGTAGCAGGTCGGCCAGATGCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGc                                                                                                                                    <  2:795237/150‑1 (MQ=255)                     gTCCTGTAGCAGGTCGGCCAGAGCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTGGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGcc                                                                                                                                   <  1:496147/150‑1 (MQ=255)                      tCCTGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGGTTCGCAAGGCTTGGGCATACTGGCGGCCGACCCACAGCAACTTCCGTTCGCGTTCGCGCTGCGCG‑GCGCTTGCCCAGATCCTCCCg                                                                                                                                  >  2:508303/1‑150 (MQ=255)                         tGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTg                                                                                                                               <  1:1041033/150‑1 (MQ=255)                         tGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTg                                                                                                                               <  2:437613/150‑1 (MQ=255)                          gTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTgg                                                                                                                              >  2:874475/1‑150 (MQ=255)                                     gCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGggcg                                                                                                                                                        >  1:222999/1‑114 (MQ=255)                                     gCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGggcg                                                                                                                                                        <  2:222999/114‑1 (MQ=255)                                      ccAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCa                                                                                                                  >  2:594428/1‑150 (MQ=255)                                      ccAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCACCAGGGCCa                                                                                                                  >  2:761456/1‑150 (MQ=255)                                       cAGATCCTGGGGGTACTGGGCCAGCCCTGGCGATGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCAc                                                                                                                 >  1:900041/1‑150 (MQ=255)                                           tCCTGGGGGTACTGGGCCAGCAATGGCGAGGCGAGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACgctg                                                                                                             >  2:741048/1‑150 (MQ=255)                                             cTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACgctgct                                                                                                           >  1:7569/1‑150 (MQ=255)                                              tGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGctactg                                                                                                          >  1:632715/1‑150 (MQ=255)                                               gggggTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGa                                                                                                         <  2:824959/150‑1 (MQ=255)                                                       tGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATc                                                                                                 >  1:865509/1‑150 (MQ=255)                                                          gCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATcagc                                                                                              >  2:437054/1‑150 (MQ=255)                                                          gCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATcagc                                                                                              >  1:780422/1‑150 (MQ=255)                                                          gCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATcagc                                                                                              <  2:115891/150‑1 (MQ=255)                                                                       aGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCa                                                                                 <  1:864351/150‑1 (MQ=255)                                                                          cgcgGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGt                                                                              <  2:900041/150‑1 (MQ=255)                                                                          cgcgGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTACTGACCGCAATCAGCAGCAGCACCCCCAGGt                                                                              <  2:632715/150‑1 (MQ=255)                                                                            cgGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTAt                                                                            <  1:98924/150‑1 (MQ=255)                                                                            cgGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTAt                                                                            <  1:321844/150‑1 (MQ=255)                                                                             ggTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATg                                                                           >  1:316360/1‑150 (MQ=255)                                                                                       gcgcAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAgccgcc                                                                 <  1:761456/150‑1 (MQ=255)                                                                                           aaGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCTCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCa                                                                                 >  2:974305/1‑130 (MQ=255)                                                                                           aaGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCTCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCa                                                                                 <  1:974305/130‑1 (MQ=255)                                                                                           aaGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTg                                                             <  2:316360/150‑1 (MQ=255)                                                                                                ttGGGCATACTGGCTGCCGACCCACAGCNACTGGCGTTCGCGGTNGNGNTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCtt                                                        >  1:786698/1‑150 (MQ=255)                                                                                                ttGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCGAGCGC‑CGCCCAgc                                                                                                                                          >  1:814522/1‑67 (MQ=38)                                                                                                ttGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCGAGCGC‑CGCCCAgc                                                                                                                                          <  2:814522/68‑2 (MQ=38)                                                                                                   ggCATACTGGCTGCCGACCCAACGCCACTGGGGTTCGGGATCGCGTCGTCTC‑GTGCCCGCCGAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCACTAAGCAGAAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTAcc                                                     <  2:865509/150‑1 (MQ=255)                                                                                                        aCTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCa                                                <  2:7569/150‑1 (MQ=255)                                                                                                             cTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGaa                                           <  1:741048/150‑1 (MQ=255)                                                                                                              tGCCGACCCACAGCAACTGGCGTTCGCGGTCGCTCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAag                                          <  1:557679/150‑1 (MQ=255)                                                                                                               gCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAaga                                         <  1:874475/150‑1 (MQ=255)                                                                                                                ccGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAagag                                        >  1:955980/1‑150 (MQ=255)                                                                                                                ccGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAagag                                        >  2:555037/1‑150 (MQ=255)                                                                                                                    cccACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTg                                    <  2:594931/150‑1 (MQ=255)                                                                                                                    cccACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTg                                    <  1:129089/150‑1 (MQ=255)                                                                                                                     ccACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGc                                   >  1:727048/1‑150 (MQ=255)                                                                                                                       acaGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGt                                                                                                                                      <  2:1094473/49‑1 (MQ=255)                                                                                                                       acaGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGt                                                                                                                                      >  1:1094473/1‑49 (MQ=255)                                                                                                                                       gcgGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGCCCTCCCtg                 <  1:594428/150‑1 (MQ=255)                                                                                                                                         ggTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCATCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAgg                                       >  2:1203386/1‑126 (MQ=255)                                                                                                                                         ggTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCATCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAgg                                       <  1:1203386/126‑1 (MQ=255)                                                                                                                                         ggTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGcc                        >  2:1172252/1‑141 (MQ=255)                                                                                                                                         ggTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGcc                        <  1:1172252/141‑1 (MQ=255)                                                                                                                                               tcTGGGCGAGCGC‑CGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGc                                                           <  1:914876/99‑1 (MQ=255)                                                                                                                                               tcTGGGCGAGCGC‑CGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGc                                                           >  2:914876/2‑100 (MQ=255)                                                                                                                                                cTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGt                                                                          >  2:55416/1‑84 (MQ=255)                                                                                                                                                cTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGt                                                                          <  1:55416/84‑1 (MQ=255)                                                                                                                                                    gcg‑gcgCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGCCCTCCCTGTGGCACCGCTCtt    <  1:480298/150‑1 (MQ=255)                                                                                                                                                      g‑gcgCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGCCCTCCCTGTGGCACCGCTCTTGa  >  2:893818/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                                      TTGGCCTGCGGGTAGCGGTTGTCCTGTAGCAGGTCGGCCAGATCCTGGGGGTACTGGGCCAGCCCTGGCGAGGCGCGGTAGTAGCTGCGCAAGGCTTGGGCATACTGGCTGCCGACCCACAGCAACTGGCGTTCGCGGTCGCGCTGGGCG‑GCGCTCGCCCAGATCGTGCCGGTGGCCGCCAGGGCCACGCTGCTGACCGCAATCAGCAGCAGCACCCCCAGGTATGTAAAGCCGCCGTTGGCCTTACCATTCAGCGAAGAGGCTGCCATCACGCGCCCTCCCTGTGGCACCGCTCTTGA  >  NC_002947/3940972‑3941270

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑