Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	975,290	A→T	13.3%	intergenic (+136/+33)	ycfJ → / ← suhB	flagella biosyntheis regulator/bifunctional inositol monophosphatase/glycerol‑2‑phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	975,290	0	A	T	13.3%	119.2 / 11.3	45	intergenic (+136/+33)	ycfJ/suhB	flagella biosyntheis regulator/bifunctional inositol monophosphatase/glycerol‑2‑phosphatase
Reads supporting (aligned to +/- strand):  ref base A (18/21);  new base T (3/3);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.62e-01

GGGTCAGTGATTTGCGGTGTCTGTGCCGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGTCGAGGAAGTC  >  NC_002947/975145‑975424                                                                                                                                                  |                                                                                                                                        gggTCAGTGATTTGCGGTGTCTGTGCCGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAagag                                                                                                                                     <  2:12487/150‑1 (MQ=255) gggTCAGTGATTTGCGGTGTCTGTGCCGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACAAGGAACAAAAAAGCACCTCAagag                                                                                                                                     <  2:12535/150‑1 (MQ=255)    tCAGTGATTTGCGGTGTCTGTGCCGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTg                                                                                                                                  >  1:496747/1‑150 (MQ=255)        tGATTTGCGGTGTCTGTGCCGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑ttt                                                                                                                             <  1:718167/150‑1 (MQ=255)                          ccGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCATTCTg                                                                                                           >  2:246329/1‑150 (MQ=255)                          ccGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTg                                                                                                           >  2:795320/1‑150 (MQ=255)                           cGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGAAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCAGAAAAAAGCACCTCAAGAGGTGC‑TTTTTGGTTGCCGGCAATCTgc                                                                                                          >  2:280194/1‑150 (MQ=255)                                        ggTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCa                                                                                             >  1:293122/1‑150 (MQ=255)                                            aaCCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCt                                                                                         <  2:496747/150‑1 (MQ=255)                                             aCCCGATCCTACAGGGGCAATGCGATCCATGCAGGCGGCGCTACACGGGCGAAGAGTTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCtt                                                                                        <  1:775968/150‑1 (MQ=255)                                              cccGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCttt                                                                                       >  2:96440/1‑150 (MQ=255)                                                   tCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTtttgt                                                                                                                         <  1:645167/111‑1 (MQ=255)                                                   tCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTtttgt                                                                                                                         >  2:645167/1‑111 (MQ=255)                                                    ccTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCACTTATGGCTTCGTGCTGGCTGGCa                                                                                 <  2:195923/150‑1 (MQ=39)                                                     cTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAg                                                                                <  2:453850/150‑1 (MQ=255)                                                      tACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTtttgttt                                                                                                                       <  2:87304/110‑1 (MQ=255)                                                      tACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTtttgttt                                                                                                                       >  1:87304/1‑110 (MQ=255)                                                           cggCAATGCGATCCATGTAGGAGCGTGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAACGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCgg                                                                          <  1:553330/149‑1 (MQ=255)                                                             gCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCt                                                                        >  1:552085/1‑150 (MQ=255)                                                              cAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTg                                                                       >  1:259866/1‑150 (MQ=255)                                                                 tGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGAt                                                                    <  1:211083/150‑1 (MQ=255)                                                                     aTCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGca                                                                <  2:293122/150‑1 (MQ=255)                                                                         aTGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCTTGAGGTGC‑ttttt                                                                                                                           <  1:751977/87‑1 (MQ=255)                                                                         aTGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCTTGAGGTGC‑ttttt                                                                                                                           >  2:751977/1‑87 (MQ=255)                                                                                           ccGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACt                                          <  1:795320/150‑1 (MQ=255)                                                                                                   agGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCATTCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTg                                  <  1:246329/150‑1 (MQ=255)                                                                                                     gTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGcc                                >  1:790415/1‑150 (MQ=255)                                                                                                         gTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCa                            >  2:27914/1‑150 (MQ=255)                                                                                                          tACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCaa                           >  1:117508/1‑150 (MQ=255)                                                                                                              ggCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCAGCGAATGGTAGTACATGCTTTCTTTTAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGAt                       <  1:96440/150‑1 (MQ=255)                                                                                                                   cGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGc                  <  2:552085/150‑1 (MQ=255)                                                                                                                    gCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGcc                 >  1:730792/1‑150 (MQ=255)                                                                                                                         accaccAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGt            <  2:428882/150‑1 (MQ=255)                                                                                                                             ccaGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGTCGAg        <  1:758395/150‑1 (MQ=255)                                                                                                                             ccaGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGTCGAg        <  1:758329/150‑1 (MQ=255)                                                                                                                                ggCGCAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGTCGGGGaa     >  1:428788/1‑150 (MQ=255)                                                                                                                                   acaAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGTCGAGGAAGTc  >  1:306461/1‑150 (MQ=255)                                                                                                                                     caaaaaGCACCTCTTGAGGTGCTTTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCaa                           <  1:166806/123‑1 (MQ=39)                                                                                                                                     caaaaaGCACCTCTTGAGGTGCTTTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCaa                           >  2:166806/2‑124 (MQ=39)                                                                                                                                     aaaaaaGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGcag                                                               <  1:399148/87‑1 (MQ=255)                                                                                                                                     aaaaaaGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGcag                                                               >  2:399148/1‑87 (MQ=255)                                                                                                                                         aaGCACCTCTTGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGaa                                               <  2:503041/99‑1 (MQ=255)                                                                                                                                         aaGCACCTCTTGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGaa                                               >  1:503041/1‑99 (MQ=255)                                                                                                                                               cTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCt                                                   <  2:711992/89‑1 (MQ=255)                                                                                                                                               cTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCt                                                   >  1:711992/1‑89 (MQ=255)                                                                                                                                                  |                                                                                                                                        GGGTCAGTGATTTGCGGTGTCTGTGCCGGCCTCTTCGCGGGTAAACCCGATCCTACAGGGGCAATGCGATCCATGTAGGAGCGGGTTTACCCGCGAAGAGGTCGGTACAGGCCACGCAAAACCACCAGGCACAAAAAAGCACCTCAAGAGGTGC‑TTTTTGTTTGCCGGCAATCTGCGCTTAGCGCTTCATGCTTTCTGGCAGGTGCGGCTGGATGGCAGTCAGTACCGCCTTGAAGCACTTGATGTTGCCTGCAACGATGTGGCCTTTGTCGAGGAAGTC  >  NC_002947/975145‑975424

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: ‑