Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,005,053	A→T	26.4%	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	26.4%	79.0 / 26.9	46	intergenic (+35/‑141)	PP_5259/ydcJ	LysR family transcriptional regulator/metalloprotein
Reads supporting (aligned to +/- strand):  ref base A (14/19);  new base T (5/7);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACCATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGC  >  NC_002947/6004905‑6005197                                                                                                                                                      |                                                                                                                                                 aaCCATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCACTCCTACGGGGAc                                                                                                                                                 <  1:200722/150‑1 (MQ=255) aaCCATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGAATTGGTCGTGTAG‑GGCAAGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGAc                                                                                                                                                 >  2:22558/1‑150 (MQ=255)         agtGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAgg                                                                                                                                         >  2:526726/3‑150 (MQ=255)           tGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGCGGTCCCCGTAggag                                                                                                                                       <  1:686/150‑3 (MQ=255)             cgcAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGagcg                                                                                                                                     <  1:526726/150‑1 (MQ=39)             cgcAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGgagc                                                                                                                                      >  1:298910/1‑149 (MQ=38)             cgcAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGgagc                                                                                                                                      <  2:298910/149‑1 (MQ=38)                     cGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGc                                                                                                                             <  2:227310/150‑1 (MQ=255)                        aGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCgg                                                                                                                          <  1:723932/150‑1 (MQ=255)                        aGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCgg                                                                                                                          <  2:159264/150‑1 (MQ=255)                              ttACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAgg                                                                                                                    <  1:308030/150‑1 (MQ=255)                              ttACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGGAGCGGCTTTAGCCGCGaagag                                                                                                                    <  2:743070/150‑4 (MQ=25)                                   tGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGt                                                                                                               >  2:345200/1‑150 (MQ=255)                                                    gCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCaaaaaa                                                                                              <  2:101937/150‑1 (MQ=255)                                                        cAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGaa                                                                                          <  1:373288/150‑1 (MQ=255)                                                        cAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGaa                                                                                          <  2:640345/150‑1 (MQ=255)                                                           agGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGa                                                                                       <  1:345200/150‑1 (MQ=255)                                                             gTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGaca                                                                                     >  2:457315/1‑150 (MQ=255)                                                                  aaaGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCaaaaaa                                                                                              <  2:318795/136‑1 (MQ=255)                                                                  aaaGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCaaaaaa                                                                                              >  1:318795/1‑136 (MQ=255)                                                                  aaaGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGgagc                                                                                                                                      >  1:117404/1‑96 (MQ=21)                                                                  aaaGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCCCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAGgagc                                                                                                                                      <  2:117404/96‑1 (MQ=21)                                                                  aaaGGTGCGGGCGCTGGTGGAATGGATTGG‑CGACAAGTTGCAGGTTTCAATGTCCCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACAcactc                                                                                >  1:149730/1‑150 (MQ=255)                                                                                tggtggAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCTCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCTCtt                                                                  >  1:647653/1‑150 (MQ=255)                                                                                  gtggAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAg                                                                                                                                          >  1:535267/1‑76 (MQ=25)                                                                                  gtggAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCGCCTACGCGGTCCCCGTAg                                                                                                                                          <  2:535267/76‑1 (MQ=21)                                                                                  gtggAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCAACGGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGTCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgt                                                                >  1:794371/1‑150 (MQ=255)                                                                                   tggAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGCGGTCCCCGTAg                                                                                                                                          <  2:3798/75‑1 (MQ=25)                                                                                   tggAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGCGGTCCCCGTAg                                                                                                                                          >  1:3798/1‑75 (MQ=25)                                                                                      aaTGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAgg                                                                                                                    >  2:557370/1‑94 (MQ=255)                                                                                      aaTGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAgg                                                                                                                    <  1:557370/94‑1 (MQ=255)                                                                                           aTTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCAATTTTTTTCGCTTGTGAGCAAAGt                                                       >  1:509092/1‑150 (MQ=255)                                                                                             tGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCAATTTTTTTCGCTTGTGAGCAAAGTGc                                                     <  2:509092/150‑1 (MQ=255)                                                                                                  gAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTc                                                 >  2:154516/1‑150 (MQ=255)                                                                                                              gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGNCCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCa                                              >  1:688101/1‑141 (MQ=255)                                                                                                              gTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCa                                              <  2:688101/141‑1 (MQ=255)                                                                                                                 tGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTaa                                  <  1:457315/150‑1 (MQ=255)                                                                                                                       ccTCTTCGGGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGACTTTAGCCGGGAAAGGGCCGTAAAAAAAAAAAAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTcc                            <  2:149730/150‑1 (MQ=255)                                                                                                                        ctctTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgt                                                                >  2:817647/1‑113 (MQ=255)                                                                                                                        ctctTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgt                                                                <  1:817647/113‑1 (MQ=255)                                                                                                                                      aGCCGCTCCTAAGGTGCCCTTGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGaa             <  2:794371/150‑1 (MQ=255)                                                                                                                                            tCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAAccc                      <  1:643753/135‑1 (MQ=255)                                                                                                                                            tCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAAccc                      >  2:643753/1‑135 (MQ=255)                                                                                                                                              cTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGa     >  1:169028/1‑150 (MQ=255)                                                                                                                                                 cGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgtg                                                               <  2:361978/89‑1 (MQ=255)                                                                                                                                                 cGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTtgtg                                                               >  1:361978/1‑89 (MQ=255)                                                                                                                                                 cGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGc  <  1:154516/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                 AACCATGCAATGCGCAGTGCCGGAGCGCATTACCTGGCGTATGCCGAGCATGCGGCAGAGGTGCCAAAGGTGCGGGCGCTGGTGGAATGGATTGG‑CGAGCAGTTGCAGGTTTGACGGCCTCTTCGCGGCTAAAGCCGCTCCTACGGGGACCGCGTAGGCGCGGCTTTAGCCGGGAAAGGGCCGTCGAGGTCGATCAAAAAAGGAATGACACACTCACTTTTTTTCGCTTGTGAGCAAAGTGCATTCCCAGCTTTCATGTAAGCGTCCGAACCCAACCAGGAAGCTAGCGATGC  >  NC_002947/6004905‑6005197

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: ‑