Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,842,896	0	C	.	24.5%	122.4 / 43.3	53	intergenic (+40/‑257)	ccoP‑II/PP_4259	cbb3‑type cytochrome c oxidase subunit/iron‑sulfur cluster‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (22/18);  new base . (7/6);  total (29/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.46e-02
Rejected as consensus: Frequency below/above cutoff threshold.

ATGCCGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGC  >  NC_002947/4842755‑4843037                                                                                                                                              |                                                                                                                                                aTGCCGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCACGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCt                                                                                                                                         <  6:269975/149‑1 (MQ=255)      ggCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCtgtg                                                                                                                                      >  1:110503/1‑144 (MQ=255)       gCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAg                                                                                                                                   <  7:45222/149‑1 (MQ=255)       gCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAg                                                                                                                                   <  2:110503/149‑1 (MQ=255)       gCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCCGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAg                                                                                                                                   <  6:24269/149‑1 (MQ=255)        cccAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGCGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCGCCTACACAGGATACG‑TGTAgg                                                                                                                                  >  6:314719/1‑149 (MQ=255)        cccAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCGGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAg                                                                                                                                   >  4:176242/1‑148 (MQ=255)        cccAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCGGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAg                                                                                                                                   >  4:176239/1‑148 (MQ=255)             gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑gg                                                                                                                            <  5:269843/149‑1 (MQ=255)             gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCGGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGctg                                                                                                                             <  3:176239/149‑3 (MQ=255)             gAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCGGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑gg                                                                                                                            <  3:176242/149‑1 (MQ=255)              aacaacTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCCGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGC‑ggg                                                                                                                           >  3:16099/1‑149 (MQ=255)                        gggCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGCTAGGTTTAccccc                                                                                                                  >  1:127576/1‑147 (MQ=255)                         ggCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑Tg                                                                                                                                      <  5:207482/128‑1 (MQ=255)                         ggCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑Tg                                                                                                                                      >  6:207482/1‑128 (MQ=255)                          gCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCCGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGC‑GGGTTTACCCGCGaa                                                                                                               <  3:112126/149‑1 (MQ=255)                                aCAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTACGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGcc                                                                                                         <  5:151091/149‑1 (MQ=255)                                             gCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAg                                                                                            >  8:108686/1‑149 (MQ=255)                                               tGGCTGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAg                                                                                                                                   <  2:14612/109‑1 (MQ=255)                                               tGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAg                                                                                                                                   >  1:14612/1‑109 (MQ=255)                                                    gattACGTCTACAGCCTGTCGCACCTGGCTGAGCCGGCCAAGGCTTAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACTGTATCCT‑TTTAGGTGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTtct                                                                                     <  4:50288/147‑1 (MQ=37)                                                      ttACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATGCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACCGCATTTCTCg                                                                                   >  5:140506/1‑149 (MQ=255)                                                         cGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCa                                                                                 <  8:215067/148‑1 (MQ=255)                                                            cTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGATGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAATCCCGCGACGAACCGGGGTGCT‑GGTAGGCGC‑GGGGTTAGGCGCGGAGGGGGGCGTACTGGCGCAGGAGTTGTCggacgc                                                                              >  6:3725/1‑143 (MQ=255)                                                              tcAGCCTGGTGCGACAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAg                                                                           >  1:100125/2‑149 (MQ=255)                                                              tcAGCCTGGTGCGACAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAg                                                                           >  8:85219/2‑149 (MQ=255)                                                               cAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCaa                                                                            <  7:108686/147‑1 (MQ=255)                                                                 gCCTGTCGCACCTGGCTGAGCCGCCCAAGGATGAGTACGGCAGGCCTGGCCTCTTCGCGGGTAACCCCGCTCCTACACAGTATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGa                                                                        <  5:3725/149‑1 (MQ=37)                                                                  ccTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCCCGCCTACACAGGATGCG‑TGTAGGGGC‑GGGTTTACCCGCGAAGAGGCCGGGAAAGGCACAGCCTTTGTCGCAGGCAAGTGAc                                                                       >  7:312781/1‑149 (MQ=37)                                                                        gCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGC‑gg                                                                                                                            <  8:247664/90‑1 (MQ=21)                                                                        gCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACA‑AGGATCCTGTGTAGGAGC‑gg                                                                                                                            >  7:247664/1‑90 (MQ=21)                                                                           ccAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCaa                                                              <  1:28272/149‑1 (MQ=255)                                                                             aGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAtt                                                            <  7:85219/149‑1 (MQ=255)                                                                                         ccAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTTAAACCCCAACAAAACACGATCCG‑TGTAGGAGC‑GGGGTTAACCGCGAAAAGGCCGGTACAGGCACAGCAATTCTGGGAGGGAAGTGACCGGGATCAATTTACACCCGCCa                                                 >  6:199011/1‑148 (MQ=255)                                                                                                  aGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCACCTACACACGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAATGACCAGGATGAATTGACACCCGCCATAACCCgat                                        >  8:163832/1‑146 (MQ=37)                                                                                                   gTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCAGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGttt                                       >  1:41120/1‑148 (MQ=255)                                                                                                    tAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGGCGGTACGGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCa                                     >  7:196614/1‑149 (MQ=255)                                                                                                         caggcCTGGCCTCTTCGCGGGTAACCCCGCTCCTACCCAGCATCCT‑TGTAGCAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCa                                <  8:19385/149‑1 (MQ=255)                                                                                                         caggcCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCa                                >  4:261090/1‑149 (MQ=255)                                                                                                                    tctTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAAcg                     >  7:65675/1‑149 (MQ=255)                                                                                                                      ttCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAtt                                                            <  5:285541/108‑1 (MQ=255)                                                                                                                      ttCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAAtt                                                            >  6:285541/1‑108 (MQ=255)                                                                                                                           gggTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGTTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTaa              <  3:309856/149‑1 (MQ=255)                                                                                                                             gTAAACCCGTTCCTACACAGTATCGT‑TTTTGGTGG‑GGTTTAACCGGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAg            <  1:148464/149‑1 (MQ=255)                                                                                                                             gTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCTTACCACGAACCCAACGCGACTAAAg            >  8:315044/1‑149 (MQ=255)                                                                                                                                 aCCCGCTCCTACA‑AGGATCCTGTGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCg        >  4:127827/1‑149 (MQ=255)                                                                                                                                  cccGCTCCTACA‑AGGATCCTGTGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATGCCACGAACCCAACGCGACTAAAGGTCGc       >  4:214590/1‑149 (MQ=255)                                                                                                                                  cccGCTCCTACA‑AGGATCCTGTGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCg        >  2:232062/1‑148 (MQ=255)                                                                                                                                   ccGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCg        >  8:150945/1‑147 (MQ=255)                                                                                                                                   ccGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCa      <  2:100125/149‑1 (MQ=255)                                                                                                                                    cGCTCCTACA‑AGGATCCTGTGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAg     >  3:168842/1‑149 (MQ=255)                                                                                                                                     gCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGAACTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGt    >  6:141798/1‑149 (MQ=255)                                                                                                                                         cTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGc  <  8:65675/147‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                ATGCCGGCCCAGGAACAACTGCAGGGCAACGACAAGGTGCACTTGCTGGCGGCTTACGTCTACAGCCTGTCGCACCAGGCTGAGCCGGCCAAGGCTGAGTAAGGCAGGCCTGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGATCCT‑TGTAGGAGC‑GGGTTTACCCGCGAAGAGGCCGGTACTGGCACAGCATTTCTCGCAGGCAAGTGACCTGGATCAATTGACACCCGCCATAACACGTTTCATACCACGAACCCAACGCGACTAAAGGTCGCAGTGC  >  NC_002947/4842755‑4843037

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: ‑