Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,950,972	T→G	16.3%	intergenic (‑122/+35)	fliL ← / ← fliK	flagellar protein FliL/flagellar hook‑length control protein FliK

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,950,972	0	T	G	16.3%	86.2 / 15.4	49	intergenic (‑122/+35)	fliL/fliK	flagellar protein FliL/flagellar hook‑length control protein FliK
Reads supporting (aligned to +/- strand):  ref base T (23/18);  new base G (3/5);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 4.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.72e-01

TCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCG  >  NC_002947/4950825‑4951118                                                                                                                                                     |                                                                                                                                                   tCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTc                                                                                                                                                   >  1:4398/1‑149 (MQ=255)     tGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGc                                                                                                                                                 <  4:20574/147‑1 (MQ=255)           cgtCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGGTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCga                                                                                                                                           <  8:327475/145‑1 (MQ=255)           cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGTGCAAGTGTTATGCCAGATTTTGC‑AGGGGGTGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaa                                                                                                                                          <  3:112439/148‑1 (MQ=255)           cTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaa                                                                                                                                          <  6:97643/148‑1 (MQ=255)              cgcgCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCgaagaa                                                                                                                                       <  4:92728/148‑1 (MQ=255)              cGCTCTTCTCCTTGCCAATAATGCGTCGTCCATGGGGGGTTCAAAGGATACTGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGG‑AGGGGATGGATTCGAGCAGGTTTTGCGGTGCTGGCTTCTTCGCCGGCTCGGGCGCgaagaa                                                                                                                                       <  2:241250/148‑1 (MQ=255)              cGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTGCAAAGGACAATGGCTTGGCTTGTGCAATTTTTATGCCATATTTTGCGCGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCgaag                                                                                                                                         <  1:112317/147‑1 (MQ=255)               gCTCTTCGCCATGCCAATAATCCGGCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGAGCCCGCGaagaag                                                                                                                                      <  3:310906/148‑1 (MQ=255)                     cGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCGCGCCCGCGAAGAagccag                                                                                                                                  <  2:141747/146‑1 (MQ=255)                      gCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGTATGGATTCCAGCAGGTTTTGAGGTGCTGGCTTCTTCGCGGGCTCGCGCGCGAAGCcgccagcc                                                                                                                                >  4:224571/1‑147 (MQ=255)                           gCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGcc                                                                                                                          >  1:333766/1‑148 (MQ=255)                            ccAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTGATGCCAGATTTTGC‑ATGGGATGGATTCCCGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCaa                                                                                                                        >  8:161762/1‑149 (MQ=255)                                  atCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTa                                                                                                                  >  1:317795/1‑149 (MQ=255)                                     cgtcgtCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTAt                                                                                                                 >  4:281124/1‑147 (MQ=255)                                      gtcttcCATCGGGGTTTCAATGGTGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGTTGTATTCCTGCAGGTTTTGCGGTGCTGGGTTCTGCGCGGGCTCGCCCGCGATGAAGCCAGCCCAGGCCAACAGTTATCAg                                                                                                              <  2:331180/149‑1 (MQ=255)                                           ccATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCgta                                                                                                         <  3:292779/149‑1 (MQ=255)                                             aTCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCCCCGGCTCGCCCCCGAACAACCCAGCCCACGCCAACAGTTATCAGGCgtag                                                                                                        >  4:192619/1‑148 (MQ=255)                                             aTCGGGGGTTCAAAGGAGAATGGCTTCGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGATTCTGAGCAGCCTCGCCCGCGAAGAAGCCAGCCAAGGCCAACAGAAATAAGGCgtag                                                                                                        >  8:284036/1‑148 (MQ=255)                                                 ggggTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATc                                                                                                   <  1:97634/149‑1 (MQ=255)                                                      tCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGGGAAGAAGCCAGCCCAGGCCAACAGTTTTAAGGCGTAGTAATCGAccc                                                                                              >  3:353391/1‑148 (MQ=255)                                                            gagaATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATAAGGCGTTGTAATCGTACGCACAGt                                                                                        >  1:184057/1‑149 (MQ=255)                                                                       ggcttgAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAac                                                                              <  2:4398/148‑1 (MQ=255)                                                                                  gtgtTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTc                                                                  <  3:281124/149‑1 (MQ=255)                                                                                  gtgtTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTc                                                                  <  2:317795/149‑1 (MQ=255)                                                                                     ttATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCa                                                                >  1:23188/1‑148 (MQ=255)                                                                                     ttATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCa                                                                >  5:304146/1‑148 (MQ=255)                                                                                          ccAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGcc                                                          >  7:194464/1‑149 (MQ=255)                                                                                            aGATTTTGC‑AGGGTATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCgg                                                        <  4:62095/149‑1 (MQ=255)                                                                                                 ttGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTTTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGgcgc                                                    <  2:333766/148‑1 (MQ=255)                                                                                                               atTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCaa                                                                                                                        <  6:71639/67‑1 (MQ=255)                                                                                                               atTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCaa                                                                                                                        >  5:71639/1‑67 (MQ=255)                                                                                                                ttCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGCCCGCTTCgg                                     >  6:375898/1‑149 (MQ=255)                                                                                                                    agcagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGAc                                             >  6:9947/1‑137 (MQ=255)                                                                                                                    agcagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGAc                                             <  5:9947/137‑1 (MQ=255)                                                                                                                     gcagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCa                                >  3:357733/1‑149 (MQ=255)                                                                                                                     gcagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCa                                >  1:76726/1‑149 (MQ=255)                                                                                                                      cagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGGCAGCCCAGGCCAACAGTTATCAGGc                                                                                                            >  3:282884/1‑72 (MQ=255)                                                                                                                      cagGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGGCAGCCCAGGCCAACAGTTATCAGGc                                                                                                            <  4:282884/72‑1 (MQ=255)                                                                                                                         gTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCt                            >  2:38684/1‑149 (MQ=255)                                                                                                                          ttttGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTACTCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGTGCGCTATCGACCGCTTCGGCCCCACCCTg                           <  7:161762/149‑1 (MQ=255)                                                                                                                          gtttGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTg                           <  3:320682/148‑1 (MQ=255)                                                                                                                                 gggCTGGCTTCTTCGCGGGCGAGCCCGCGAAGCAGCCAGCCCAGGCCACCAGTTATCAGGGGTAGTAATCGACCGCACTGTCGCCGCCAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGcc                    >  5:112286/3‑149 (MQ=39)                                                                                                                                         ttcttcGCGGGCGAGCCCGCGAAGAAGCCAGCACAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGgcgcgc            >  1:38735/1‑149 (MQ=255)                                                                                                                                          tcttcGCGGGCGAGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCCCCTGCTGCTCCAACGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgcc           >  6:229529/1‑149 (MQ=255)                                                                                                                                           cttcGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgcc           <  4:353391/148‑1 (MQ=255)                                                                                                                                            ttcGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACCACCACCTGCTGCTCCAACGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgccgc         >  2:172956/1‑149 (MQ=255)                                                                                                                                            ttcGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGcgccgc         >  1:327824/1‑149 (MQ=255)                                                                                                                                                    cTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAACGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCg  >  8:217390/1‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                   TCTTTGACTGCTTCGCTCTTCGCCATGCCAATAATCCGTCGTCCATCGGGGGTTCAAAGGAGAATGGCTTGGCTTGAGCAAGTGTTATGCCAGATTTTGC‑AGGGGATGGATTCCAGCAGGTTTTGCGGTGCTGGCTTCTTCGCGGGCTCGCCCGCGAAGAAGCCAGCCCAGGCCAACAGTTATCAGGCGTAGTAATCGACCGCACTGTCGCCGACAACCACCTGCTGCTCCAAAGGCCGGGCGCTATCGACCGCTTCGGCCCCACCCTGCTCGGCCCGGCGCGCCGCCACCCCG  >  NC_002947/4950825‑4951118

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: ‑