Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,005,053	A→T	12.8%	intergenic (+35/‑141)	PP_5259 → / → ydcJ	LysR family transcriptional regulator/metalloprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,005,053	0	A	T	12.8%	131.8 / 10.9	47	intergenic (+35/‑141)	PP_5259/ydcJ	LysR family transcriptional regulator/metalloprotein
Reads supporting (aligned to +/- strand):  ref base A (19/22);  new base T (2/4);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 6.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.37e-01

CCATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGCCCGCC  >  NC_002947/6004907‑6005202                                                                                                                                                   |                                                                                                                                                      ccATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACcg                                                                                                                                                    >  1:63560/1‑150 (MQ=255)   aTGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACcgcg                                                                                                                                                  >  1:997118/1‑150 (MQ=255)      cAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCCTTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAg                                                                                                                                               <  1:465847/150‑1 (MQ=37)        aTGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGCGGTCCCCGTAgga                                                                                                                                             <  1:1179116/150‑2 (MQ=255)          gcgcAGTGCCGGAGCGCATTACCTGGCGTGGGGCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGTTCCTACGGGGACCGCGTAGgcgc                                                                                                                                           <  1:907741/150‑1 (MQ=255)          gcgcAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGgcgc                                                                                                                                           <  2:614551/150‑1 (MQ=255)                          cATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCAGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGaaa                                                                                                                           >  2:540251/1‑150 (MQ=255)                              aCCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGc                                                                                                                       <  1:768883/150‑1 (MQ=255)                               ccTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCAGGGAAAGGGcc                                                                                                                      <  1:88055/150‑1 (MQ=255)                                 tGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCggg                                                                                                                              >  1:112409/1‑140 (MQ=255)                                 tGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCggg                                                                                                                              <  2:112409/140‑1 (MQ=255)                                 tGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGt                                                                                                                    >  1:263559/1‑150 (MQ=255)                                              gCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAAAGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCaa                                                                                                       >  1:1150060/1‑150 (MQ=255)                                                               cAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACAcact                                                                                      >  1:909621/1‑150 (MQ=255)                                                                aaaGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGACTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGaca                                                                                          >  2:544777/1‑145 (MQ=255)                                                                aaaGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGACTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGaca                                                                                          <  1:544777/145‑1 (MQ=255)                                                                         ggCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACttttttt                                                                            <  2:63560/150‑1 (MQ=255)                                                                         ggCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCgg                                                                                                                                         <  2:918054/89‑1 (MQ=21)                                                                         ggCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCgg                                                                                                                                         >  1:918054/1‑89 (MQ=21)                                                                          gcgcTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTc                                                                           >  2:446553/1‑150 (MQ=255)                                                                            gcTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGc                                                                         <  2:437718/150‑1 (MQ=255)                                                                                 tggAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTACGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgtg                                                                    <  1:446553/150‑1 (MQ=255)                                                                                  ggAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGa                                                                   <  2:1150060/150‑1 (MQ=255)                                                                                    aaTGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACttttt                                                                              <  1:751617/137‑1 (MQ=255)                                                                                    aaTGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACttttt                                                                              >  2:751617/1‑137 (MQ=255)                                                                                       ggATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCaaa                                                              <  2:263559/150‑1 (MQ=255)                                                                                               gagaAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCTCTTTTGAGCAAAGTGCATTc                                                      >  2:444168/1‑150 (MQ=255)                                                                                                 gCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGacaca                                                                                        <  2:263515/114‑1 (MQ=255)                                                                                                 gCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGacaca                                                                                        >  1:263515/1‑114 (MQ=255)                                                                                                  cAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCaaaaaa                                                                                                   >  1:586643/1‑102 (MQ=255)                                                                                                  cAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCaaaaaa                                                                                                   <  2:586643/102‑1 (MQ=255)                                                                                                    gTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCttt                                                                                                                                     >  2:894035/1‑66 (MQ=255)                                                                                                    gTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCttt                                                                                                                                     <  1:894035/66‑1 (MQ=255)                                                                                                     ttGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGa                                                                                            >  1:52365/1‑106 (MQ=255)                                                                                                     ttGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGa                                                                                            <  2:52365/106‑1 (MQ=255)                                                                                                     ttGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCt                                                >  1:770707/1‑150 (MQ=255)                                                                                                           gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGacac                                                                                         >  1:70427/1‑103 (MQ=255)                                                                                                           gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGacac                                                                                         <  2:70427/103‑1 (MQ=255)                                                                                                            tttGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGt                                         <  2:997118/150‑1 (MQ=255)                                                                                                              tGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTaa                                       <  2:770707/150‑1 (MQ=255)                                                                                                                  ggCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGt                                   >  2:511785/1‑150 (MQ=255)                                                                                                                    ccTCTTCGCGGCTAAAGCCGATCCTACGGAGACCGCGTAGGTGTGGCTTTAGCAGGGAAAGGGCCGTTGAGAACAAAAAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCTCAGTTTTCAGGTAAGCGTcc                                 <  2:356453/150‑1 (MQ=255)                                                                                                                           ccgGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgt                                                                     >  2:629899/2‑107 (MQ=21)                                                                                                                           ccgGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgt                                                                     <  1:629899/106‑1 (MQ=21)                                                                                                                             ggCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAAc                        <  1:540251/150‑1 (MQ=255)                                                                                                                               cTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCa                      <  2:42980/150‑1 (MQ=255)                                                                                                                                           cTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGCAGTGCCTGAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGa          >  2:897063/1‑150 (MQ=255)                                                                                                                                                   aCCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCGAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATCCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGCCCGcc  >  1:852993/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                      CCATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGGCGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGCCCGCC  >  NC_002947/6004907‑6005202

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑