Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,603,077	A→C	12.4%	K12Q (AAG→CAG) ‡	PP_5513 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,603,077	0	A	C	12.4%	135.0 / 9.4	54	K12Q (AAG→CAG) ‡	PP_5513	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (24/22);  new base C (4/3);  total (28/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.63e-01

AGGCGATGAGCGATAAGCGCTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCCCGTCCGTTCTGGTCAC  >  NC_002947/2602931‑2603224                                                                                                                                                     |                                                                                                                                                    aGGCGATGAGCGATAAGCGCTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCaa                                                                                                                                                    <  1:214958/148‑1 (MQ=255)  ggCGATGAGCGATAAGCGCTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGt                                                                                                                                                  <  5:112927/149‑1 (MQ=255)          gCGATAAGCGCTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGtggatgga                                                                                                                                           <  5:239166/148‑1 (MQ=255)                aGCGCTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTg                                                                                                                                    >  3:24465/1‑149 (MQ=255)                 gcgcTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCCACTTGATggagaa                                                                                                                                        <  7:263356/144‑3 (MQ=255)                 gcgcTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCCACTTGATggagaa                                                                                                                                        >  8:263356/1‑142 (MQ=255)                 gcgcTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTg                                                                                                                                    >  7:24169/1‑148 (MQ=255)                  cgcTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCCACTTGATGGA‑GAAGTgttc                                                                                                                                 <  8:91658/149‑4 (MQ=255)                   gcttacGCAGTGACCTGGCATACCGTGCCCGTGTCCATGTCTAGCTCCTTCGTTCCAAAGTCTTTTTATGCCTGGCCGTAATAAGAAAAACA‑ACAATGTGCGGTTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGa                                                                                                                                  <  8:238314/143‑1 (MQ=255)                   gcTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGAt                                                                                                                                 >  4:160272/1‑149 (MQ=255)                     tACCGAATTGACCCGGCATACCCTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCAAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATTAGCTGCATCAACGACGAACACTT‑CACCATCAAGTTGATGGAGTAAGTCGAttt                                                                                                                               >  6:29152/1‑147 (MQ=255)                          cAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTgg                                                                                                                          <  2:294138/149‑1 (MQ=255)                           aGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGa                                                                                                                         >  7:277940/1‑149 (MQ=255)                            gTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGaa                                                                                                                                       >  5:180641/1‑134 (MQ=255)                            gTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGaa                                                                                                                                       <  6:180641/134‑1 (MQ=255)                                cccGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGactact                                                                                                                    >  1:224968/1‑149 (MQ=255)                                         ccGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCtt                                                                                                           <  8:104668/149‑1 (MQ=255)                                            tGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGc                                                                                                        <  6:27219/149‑1 (MQ=255)                                                    tCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTggg                                                                                                                 <  8:69097/132‑1 (MQ=255)                                                    tCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTggg                                                                                                                 >  7:69097/1‑132 (MQ=255)                                                      cAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCt                                                                                               <  3:160272/148‑1 (MQ=255)                                                      cAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTa                                                                                              <  4:24465/149‑1 (MQ=255)                                                         gCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACAGACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTaat                                                                                            >  1:99330/1‑147 (MQ=255)                                                           cAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTgg                                                                                                                          <  4:280213/116‑1 (MQ=255)                                                           cAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTgg                                                                                          >  1:182073/1‑148 (MQ=255)                                                           cAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGa                                                                                         >  5:121289/1‑149 (MQ=255)                                                           cAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACAT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTgg                                                                                                                          >  3:280213/1‑116 (MQ=255)                                                                   tccGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTccc                                                                                 >  4:7948/1‑149 (MQ=255)                                                                   tccGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTccc                                                                                 >  6:204954/1‑149 (MQ=255)                                                                      gTTCCAACGTCTTCTGACGCCTGGCCGCAATTAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGaa                                                                              <  5:204954/149‑1 (MQ=255)                                                                           aaCGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCCACTTGATggagaa                                                                                                                                        >  5:380430/1‑84 (MQ=255)                                                                           aaCGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCCACTTGATggagaa                                                                                                                                        <  6:380430/86‑3 (MQ=255)                                                                              gTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTgg                                                                      >  4:268898/1‑149 (MQ=255)                                                                               tcttctGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGc                                                                     <  2:182073/149‑1 (MQ=255)                                                                                   ctGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCg                                                                   <  8:54514/147‑1 (MQ=255)                                                                                           tGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGAt                                                         >  5:240376/1‑149 (MQ=255)                                                                                             gCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGt                                                       >  2:67059/1‑149 (MQ=255)                                                                                                  aaTAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCg                                                  >  8:249924/1‑149 (MQ=255)                                                                                                  aaTAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCg                                                  >  3:243595/1‑149 (MQ=255)                                                                                                      aGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTg                                               <  6:313414/148‑1 (MQ=255)                                                                                                      aGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTg                                               >  5:313414/1‑148 (MQ=255)                                                                                                       gAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCAGCTGGc                                             >  3:113130/1‑149 (MQ=255)                                                                                                           aaca‑acAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTtca                                         <  3:7948/149‑1 (MQ=255)                                                                                                              a‑acaaTGAGCGGCTTCACCGACGCACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGTCTtcatca                                      >  6:248391/1‑149 (MQ=255)                                                                                                                    tGAGCGGCTTAAACGACGAACACTT‑ATCCCTCCAGTGGATGGAGGAAGTGGATGGCGTGGACTTATGGGCATATTCGCCTTTCCGATAGTGGATCGGTCCCGAATGGACTGGCCGGTACGTGGATGTCCCAGCTGGCGTCATCACTGAt                                 >  6:70870/1‑149 (MQ=255)                                                                                                                         ggCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGc                            <  6:240376/149‑1 (MQ=255)                                                                                                                              cACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTc                         <  2:224968/147‑1 (MQ=255)                                                                                                                              cACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCt                        <  8:277940/148‑1 (MQ=255)                                                                                                                                    catccacTTCCTCCATCCACTTGATGGAGAAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTAccc                  >  1:141931/5‑149 (MQ=255)                                                                                                                                      aaCACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCccgt               <  6:121289/149‑1 (MQ=255)                                                                                                                                        cagtt‑CTCCTTCTAGTGGATGGAGGAAGTGGATGGCGTTGATTACTGTTCATCTTCTCCTTTCCGCTACTGGATCGGTCCCGAAGGTACTTGCCGGTACGTGGATGTCGGCGCTGGCTTCATCACTGATGGAGCTTCTGTACCccgtcc             <  8:24169/146‑1 (MQ=255)                                                                                                                                         acTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCccgtccg            >  5:389594/1‑149 (MQ=255)                                                                                                                                          cTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCccgtccgt           >  5:156153/1‑149 (MQ=255)                                                                                                                                                ccATGATGTGGATTGAGGTAGTTGATGGCGTGGACTACTTGGAATCTTCGCCTTTCCGCTACTTGATCGGTCCAGTAGGGAGTGGCCTGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCCCGTCCGTTCTg       <  5:29152/148‑1 (MQ=255)                                                                                                                                                 gttCATGTGGTTTGAGGAAGTGGATGTGGTGGACTACTGGGCTTCTTCTCCTTTGCGCTAGTGGATCGGTCCCGCAGGGACTGGCCGGTACGTGGATGTCGCCGCTGGCTTCATCACTGTTGGAGCTTCTGTACCCCGTCCGTTCTgt      <  4:113130/146‑2 (MQ=255)                                                                                                                                                     aaGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCCCGTCCGTTCTGGTCAc  <  7:249924/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                    AGGCGATGAGCGATAAGCGCTACCGCAGTGACCCGGCATACCGTGCCCGAGTCCAGGCCAAGCTCCTCCGTTCCAACGTCTTCTGACGCCTGGCCGCAATAAGAAAAACA‑ACAATGAGCGGCTTCACCGACGAACACTT‑CTCCATCAAGTGGATGGAGGAAGTGGATGGCGTGGACTACTGGGCATCTTCGCCTTTCCGCTACTGGATCGGTCCCGAAGGGACTGGCCGGTACGTGGATGTCCCCGCTGGCTTCATCACTGATGGAGCTTCTGTACCCCGTCCGTTCTGGTCAC  >  NC_002947/2602931‑2603224

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: ‑