Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,993,604	A→C	19.6%	intergenic (+42/+56)	PP_1780 → / ← PP_1781	mannosyltransferase/acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,993,604	0	A	C	19.6%	115.8 / 26.8	56	intergenic (+42/+56)	PP_1780/PP_1781	mannosyltransferase/acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (22/23);  new base C (4/7);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 5.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.38e-01

CTTGGCTACATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCGGTGGGTCAACAGGCTTAGCGG  >  NC_002947/1993459‑1993749                                                                                                                                                  |                                                                                                                                                   cTTGGCTACATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGcc                                                                                                                                                 <  4:241197/149‑1 (MQ=255)       tACATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCa                                                                                                                                              >  5:341608/1‑146 (MQ=255)       tACATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCa                                                                                                                                              <  6:341608/146‑1 (MQ=255)        aCATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTg                                                                                                                                           >  8:84741/1‑148 (MQ=255)        aCATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTg                                                                                                                                           >  6:269159/1‑148 (MQ=255)        aCATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCAACCATGAACCCTGCAGTGCGGCTGCGCCGCACt                                                                                                                                            >  5:24807/1‑147 (MQ=255)        aCATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCAACCATGAACCCTGCAGTGCGGCTGCGCCGCACt                                                                                                                                            <  6:24807/147‑1 (MQ=255)         cATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCTGCGCCGCACTGCa                                                                                                                                         <  7:233898/149‑1 (MQ=255)         cATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCTGCGCCGCACTGCa                                                                                                                                         <  3:291112/149‑1 (MQ=255)         cATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCTGCGCCGCACTGCa                                                                                                                                         <  5:47523/149‑1 (MQ=255)                   ataGTGGAGCTGATCTATTAGGGCTGGTGTTGGATGTTACGGTAAATACTCAGCTGAATCATAAGGCGCCTGCTGTAGCGCACTGATTGCGTACGCTTTGCCATCCATGAAGCCTGCTGTGCGGCGCAGCCGGTGTGGA‑GGGCTTTTg                                                                                                                               <  4:45283/146‑1 (MQ=255)                   aaaGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGc                                                                                                                              <  1:184040/149‑1 (MQ=255)                       tGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCTATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCttt                                                                                                                                 >  2:43415/1‑142 (MQ=255)                       tGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCAATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCttt                                                                                                                                 <  1:43415/142‑1 (MQ=255)                             tGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACtt                                                                                                                    >  4:78747/1‑149 (MQ=255)                               aaCTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGt                                                                                                                  <  5:269159/149‑1 (MQ=255)                                   aaaaCGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGACATCCATGAACCCTGCAGTGCGGCGTAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTAt                                                                                                                >  8:71509/1‑147 (MQ=255)                                    aaaCGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCTCACTGATTGCGTACGCTTGGCCATCCAGCAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAg                                                                                                             <  3:345784/149‑1 (MQ=255)                                              tgtTGGATGTTACGGAAAATACTCAGCTGAAGCATAAAGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGt                                                                                                    >  1:245077/1‑148 (MQ=255)                                                ttGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTaaa                                                                                                 <  3:78747/149‑1 (MQ=255)                                                  ggATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAAcg                                                                                               >  3:220253/1‑149 (MQ=255)                                                    aTGTTACGTAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAAcgcg                                                                                             <  3:31013/149‑1 (MQ=255)                                                     tGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACgcgc                                                                                            <  7:84741/149‑1 (MQ=255)                                                        tACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGAGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTa                                                                                         >  5:119689/1‑149 (MQ=255)                                                              aaaTACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGc                                                                                   >  8:19071/1‑149 (MQ=255)                                                                       gCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGTAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGcac                                                                          <  7:71509/149‑1 (MQ=255)                                                                          gAAGCATAAGGCGCCTGCTAAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAgg                                                                                                            <  1:165268/112‑1 (MQ=255)                                                                          gAAGCATAAGGCGCCTGCTAAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAgg                                                                                                            >  2:165268/1‑112 (MQ=255)                                                                           aaGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGcc                                                                      <  7:19071/149‑1 (MQ=255)                                                                             gCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCa                                                                                                      <  8:6902/115‑1 (MQ=255)                                                                             gCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCa                                                                                                      >  7:6902/1‑115 (MQ=255)                                                                             gCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTg                                                                    <  3:249670/149‑1 (MQ=255)                                                                                   ggCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACg                                                              >  6:124737/1‑149 (MQ=255)                                                                                   ggCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACg                                                              <  7:222628/149‑1 (MQ=255)                                                                                    gcgcCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGc                                                             >  6:272110/1‑149 (MQ=255)                                                                                      gcCTGCTCAAGCGCACTGATTGCGTACGGTTGGCCATCCATGAACCCTGCAGTGCGGCGAAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTg                                                           <  5:50326/149‑1 (MQ=255)                                                                                      gcCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCAAAGCCTGGCGACGCTg                                                           >  7:273782/1‑149 (MQ=255)                                                                                       ccTGCTCATCCGCCCTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTgg                                                          <  6:119689/149‑1 (MQ=255)                                                                                                        aTTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGa                                           <  7:125551/147‑1 (MQ=255)                                                                                                        aTTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAg                                          <  5:124737/148‑1 (MQ=255)                                                                                                                      gCCATCCATGAACCCTGCAGTGCGGCGTAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTccagc                            >  4:223970/1‑148 (MQ=255)                                                                                                                       ccatccatGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTccagc                            >  7:124844/1‑147 (MQ=255)                                                                                                                               gAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGgcg                                                        >  2:163491/1‑111 (MQ=255)                                                                                                                               gAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGgcg                                                        <  1:163491/111‑1 (MQ=255)                                                                                                                                    cTGCAGTGCGGCTGCGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTcca                              <  6:285174/132‑1 (MQ=255)                                                                                                                                    cTGCAGTGCGGCTGCGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTcca                              >  5:285174/1‑132 (MQ=255)                                                                                                                                    cTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCgg                      <  3:327817/140‑1 (MQ=255)                                                                                                                                    cTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCgg                      >  4:327817/1‑140 (MQ=255)                                                                                                                                     tGCAGTGCGGCTGCGCCGCACTGCAGGGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCGGTg                    >  1:184913/1‑142 (MQ=255)                                                                                                                                     tGCAGTGCGGCTGCGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCGGTg                    <  2:184913/141‑1 (MQ=255)                                                                                                                                     tGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCGGTGGGTCaa              >  8:195692/1‑147 (MQ=255)                                                                                                                                        aGTGCGGCTGCGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGc                                                                       <  6:120295/87‑1 (MQ=39)                                                                                                                                        aGTGCGGCTGCGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGc                                                                       >  5:120295/1‑87 (MQ=39)                                                                                                                                               cgcAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCGGTGGGTCAACAGGCTTAGCgg  >  1:248868/1‑149 (MQ=255)                                                                                                                                                 cAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGcac                                                                          >  6:278798/1‑75 (MQ=255)                                                                                                                                                 cAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGcac                                                                          <  5:278798/75‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                   CTTGGCTACATTGGAGTGAAAGTGCAGCTGAACTAAAACGCCTGGTGTTGGATGTTACGGAAAATACTCAGCTGAAGCATAAGGCGCCTGCTCAAGCGCACTGATTGCGTACGCTTGGCCATCCATGAACCCTGCAGTGCGGCGCAGCCGCACTGCA‑GGGCTTTTGCCATATGACTTGTATGAGGCACGCAGTAAACGCGCTTATCCGGCTACGGGCACAGCCTGGCGACGCTGGCGCAGATAGCGTTGAGCCGGGCGTTCCAGCCAGCGGTGGGTCAACAGGCTTAGCGG  >  NC_002947/1993459‑1993749

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: ‑