Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,839,269	C→G	14.3%	intergenic (+46/‑134)	ccoP‑I → / → PP_4254	cbb3‑type cytochrome c oxidase subunit/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,839,269	0	C	G	14.3%	151.7 / 17.6	56	intergenic (+46/‑134)	ccoP‑I/PP_4254	cbb3‑type cytochrome c oxidase subunit/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (19/29);  new base G (2/6);  total (21/35)
Fisher's exact test for biased strand distribution p-value = 6.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.62e-01

GGCGCAGGCCGAGATCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCAAACCATACCCCCACCGCCGCCCCCTTCCCTTGCACCCCCACCGAACACAACTAAGCTTGTTGCCTCAGT  >  NC_002947/4839121‑4839404                                                                                                                                                      |                                                                                                                                        ggCGCAGGCCGAGATCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCcgcg                                                                                                                                        >  2:652851/1‑150 (MQ=255)  gcgcAGGCCGAGATCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCcgcgc                                                                                                                                       <  1:652851/150‑1 (MQ=255)       ggCCGAGATCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGC‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGgcgc                                                                                                                                  <  2:458167/150‑1 (MQ=255)         ccGAGATCCAGGGGAATGACATGGTGCAGGTCCGGGCGGCTTAAGTGTATAGCATGATGACGTACTGATGCTG‑TTATGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTc                                                                                                                                <  1:1252008/150‑1 (MQ=19)         ccGAGATCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTc                                                                                                                                <  1:242617/150‑1 (MQ=255)            agaTCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGat                                                                                                                             <  2:2138317/150‑1 (MQ=255)            agaTCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGat                                                                                                                             <  2:1060698/150‑1 (MQ=255)              aTCCAGGGGTCAGACAAGTGGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGAAGGA‑TGCTGGTGTTTAAGCTGGGCCGGCCAAGTGACTTCGCAGAAACCAATTTGCAGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGatat                                                                                                                           <  1:2350744/150‑1 (MQ=19)               tCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATc                                                                                                                          <  2:365721/150‑1 (MQ=255)                  aGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGTCTGTGAGATCGAGCGCCGCGCGGGCGGCGCTCGAtctcaca                                                                                                                       <  1:664055/150‑4 (MQ=38)                        aTGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCccacc                                                                                                                 <  1:720602/150‑1 (MQ=255)                            cAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGc                                                                                                                       <  1:439509/140‑1 (MQ=255)                            cAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGc                                                                                                                       >  2:439509/1‑140 (MQ=255)                            cAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATaa                                                                                                             <  1:508860/150‑1 (MQ=255)                                gTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCAt                                                                                                         <  2:1095230/150‑1 (MQ=255)                                      ctgctgGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCAt                                                                                                         <  2:2298180/144‑1 (MQ=255)                                      ctgctgGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCAGAACCAt                                                                                                         >  1:2298180/1‑144 (MQ=255)                                       tgctgGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCt                                                                                                  <  2:2051196/150‑1 (MQ=255)                                          tgGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTac                                                                                               >  1:1519636/1‑150 (MQ=255)                                            gcggcTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCTCCCGCGCGGCGCTCTGTATCGGCCGCACCATAAACTTCAAACCTTccac                                                                                             >  2:331960/1‑150 (MQ=255)                                                     gtgtATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATc                                                                                                        <  1:268508/130‑1 (MQ=255)                                                     gtgtATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATc                                                                                                        >  2:268508/1‑130 (MQ=255)                                                     gtgtATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGcccc                                                                                    <  2:1977303/150‑1 (MQ=255)                                                     gtgtATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGcccc                                                                                    >  2:502398/1‑150 (MQ=255)                                                       gtATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCccac                                                                                  <  1:1452807/150‑1 (MQ=255)                                                        tataGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACAccccccccccccc                                                                                 >  1:1850755/1‑147 (MQ=255)                                                         ataGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCTATATTCGCCCCACCAAAACCAACAAACCTTACAACcccccccccgca                                                                                >  1:2021434/1‑146 (MQ=38)                                                            gCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATcc                                                                             <  1:502398/150‑1 (MQ=255)                                                             ccTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCAACAAACCTTACCACCCCCCCccaccccaat                                                                            >  1:1691243/1‑145 (MQ=39)                                                                   gCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCAt                                                                                                         >  1:1988607/1‑115 (MQ=255)                                                                   gCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCAt                                                                                                         <  2:1988607/115‑1 (MQ=255)                                                                    cAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCaaa                                                                     <  1:895701/150‑1 (MQ=255)                                                                             ttCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTac                                                                                               >  2:751290/1‑116 (MQ=255)                                                                             ttCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTac                                                                                               <  1:751290/116‑1 (MQ=255)                                                                             ttCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTac                                                                                               <  1:197115/116‑1 (MQ=255)                                                                             ttCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGACGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTac                                                                                               >  2:197115/1‑116 (MQ=255)                                                                                       gCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCgcggc                                                                                                                                    <  1:2299303/69‑1 (MQ=255)                                                                                       gCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCgcggc                                                                                                                                    >  2:2299303/1‑69 (MQ=255)                                                                                         tgtgACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGATATCGAGCGCCGCGCGGGCGGCGCTc                                                                                                                                <  2:1368312/71‑1 (MQ=25)                                                                                         tgtgACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGATATCGAGCGCCGCGCGGGCGGCGCTc                                                                                                                                >  1:1368312/1‑71 (MQ=25)                                                                                                         gTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTaca                                                                                              <  2:1487737/89‑1 (MQ=255)                                                                                                         gTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTaca                                                                                              >  1:1487737/1‑89 (MQ=255)                                                                                                            cGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAAcc                                                                                                           <  1:1492082/73‑1 (MQ=255)                                                                                                            cGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAAcc                                                                                                           >  2:1492082/1‑73 (MQ=255)                                                                                                             gCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCccac                                                                                  <  1:574815/97‑1 (MQ=255)                                                                                                             gCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCccac                                                                                  >  2:574815/1‑97 (MQ=255)                                                                                                                gAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCccac                                                                                  <  2:180848/94‑1 (MQ=255)                                                                                                                gAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCccac                                                                                  >  1:180848/1‑94 (MQ=255)                                                                                                                gAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCAAACCATACCCCCACCGCCGCCCCCTTCCCTTGCACCCCCACCGaa                          <  1:2013594/150‑1 (MQ=255)                                                                                                                     gCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCAAACCATACCCCCACCGCCGCCCCCTTCCCTTGCACCCCCACCGAACACaa                     <  1:569282/150‑1 (MQ=255)                                                                                                                     gCATTTGCCGCCGGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCAAACCATACCCCCACCGCCGCCCCCTTCCCTTGCACCCCCACCGAACACaa                     <  2:301763/150‑1 (MQ=255)                                                                                                                             cgccTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACAccccc                                                                                         <  2:1572273/74‑1 (MQ=255)                                                                                                                             cgccTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACAccccc                                                                                         >  1:1572273/1‑74 (MQ=255)                                                                                                                                        tCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGccc                                                                                     >  2:2196060/1‑67 (MQ=255)                                                                                                                                        tCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGccc                                                                                     <  1:2196060/67‑1 (MQ=255)                                                                                                                                        gcGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCAAACCATACCCCCACCGCCGCCCCCTTCCCTTGCACCCCCACCGAACACAACTAAGCTTGTTGCCTCAGt  <  2:890964/149‑1 (MQ=255)                                                                                                                                           aGCGCCGCGCGGGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATc                                                                              <  2:1266410/71‑1 (MQ=37)                                                                                                                                           aGCGCCGCGCGGGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATc                                                                              >  1:1266410/1‑71 (MQ=37)                                                                                                                                                      |                                                                                                                                        GGCGCAGGCCGAGATCCAGGGGAATGACAAGGTGCACCTGCTGGCGGCTTACGTGTATAGCCTGTCGCAGGA‑TGGTTCGGCTGAGGCTGTGACGGCCAAGTGAGTTCGCCGAAAGGCATTTGCCGCCTGTGAGATCGAGCGCCGCCCGCGCGGCGCTCGATATCCGCCCCACCATAACCATCAAACCTTACACCCCCGCCCCACCATCCCCCTCAAACCATACCCCCACCGCCGCCCCCTTCCCTTGCACCCCCACCGAACACAACTAAGCTTGTTGCCTCAGT  >  NC_002947/4839121‑4839404

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: ‑