Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,657,881	G→T	16.8%	intergenic (+315/+104)	hdeD → / ← arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,657,881	0	G	T	16.8%	106.3 / 3.0	49	intergenic (+315/+104)	hdeD/arrS	acid‑resistance membrane protein/antisense sRNA ArrS, function unknown
Reads supporting (aligned to +/- strand):  ref base G (24/15);  new base T (7/2);  total (32/17)
Fisher's exact test for biased strand distribution p-value = 4.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCAAATTAGCCATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGA  >  NC_000913/3657733‑3658029                                                                                                                                                     |                                                                                                                                                      ggaaaaTTAGCCATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTg                                                                                                                                                       <  2:330902/146‑1 (MQ=255) ggCAAATTACCCATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTg                                                                                                                                                       <  2:243877/149‑1 (MQ=255)   cAAATTAGCCATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCa                                                                                                                                                     >  1:563548/1‑149 (MQ=255)         ggCCAGTTCAAACATTATCAGGGCTGATATTTTCCGTAGTCAGGTTTATTGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGc                                                                                                                                               <  1:202565/148‑1 (MQ=255)           ccATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCaattttcgt                                                                                                                                             >  2:193718/1‑142 (MQ=255)           ccATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGt                                                                                                                                             >  2:240576/1‑149 (MQ=255)              tttCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGa                                                                                                                                          <  1:634340/149‑1 (MQ=255)              tttCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGa                                                                                                                                          <  1:58526/149‑1 (MQ=255)              tttCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGGTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGa                                                                                                                                          >  2:643146/1‑149 (MQ=255)                    aCATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCATGGATTACAt                                                                                                                                    >  1:53432/1‑149 (MQ=255)                     cagtATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACAtt                                                                                                                                   <  1:66635/146‑1 (MQ=255)                        tATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCa                                                                                                                                <  1:338033/149‑1 (MQ=255)                            aTGGCTGATATTTTCCGTAGTCAGGTTTCATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATaaa                                                                                                                            >  1:391461/1‑149 (MQ=255)                             tGGCTTATATTGTCCGTAGTGAGGTTTAATGTTTTAAAAGTGCTGTGGGAACGGCAAAAAAGAGTTCGGTAAGCGTTGATGCTAGGGGTGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAAGTGGCGTTGATTACATTGCATAAat                                                                                                                           <  2:171172/149‑1 (MQ=255)                             tGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAat                                                                                                                           <  2:102195/149‑1 (MQ=255)                                   atatTTTCCGTAGTCAGGTTGAATGTTTTAAAAGTGCTGTGGGAAAGTGAGCAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATCAGTAATCGAGGTTCATTTTTTTTCAACTGGCGTTGATTACATTGCATAAATATCCgt                                                                                                                     <  2:158361/149‑1 (MQ=255)                                                tCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAATGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCt                                                                                                       >  1:469026/1‑149 (MQ=255)                                                  aGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTTCATCTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCtat                                                                                                     >  2:439538/1‑149 (MQ=255)                                                  aGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTCGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCtat                                                                                                     <  1:24480/149‑1 (MQ=255)                                                  aGGTTTAAGGTTCTCACCGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCtat                                                                                                     <  2:115264/149‑1 (MQ=255)                                                    gTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCtatat                                                                                                   >  1:657508/1‑149 (MQ=255)                                                         aTGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAGTCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATagaaa                                                                                              >  2:225194/1‑149 (MQ=255)                                                                aaaaGTGCTGTGGGAAAGTGAACAAAGAGTTCGGTAAGCGTTTATGGTATGGGGGGGTAAATAAGTAAGGCGGGATCATTTTTTTTCAACTGGCGTTGATTACATTGCTTAAATATCCATTACTCCAG‑ACCGTAGATAACAACCTGaat                                                                                       >  2:367208/1‑148 (MQ=255)                                                                aaaaGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAg                                                                                       >  2:719614/1‑149 (MQ=255)                                                                         gtgGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTCATCCGGGTTCATTTTTTTGCAACTGGCGTGGATTACATTGCCTAAATATTCGTGTCTACAG‑TCGCTATATAAAAACCTGAAGACATGAAtt                                                                              >  1:52194/1‑148 (MQ=255)                                                                             gAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGtt                                                                          >  1:45835/1‑149 (MQ=255)                                                                              aaaGTGAACAAAGAGTTCCGTAAGCGTAGCTGCTATGAGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTa                                                                         >  1:358431/1‑149 (MQ=255)                                                                                       aaaGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATACAAACCTGAAGACATGAATGCGTTATTTACTCAg                                                                <  1:472307/149‑1 (MQ=255)                                                                                        aaGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTTCTTTTTTTGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGATGACATGAATGCGTTATTTACTCAgg                                                               >  2:669445/1‑149 (MQ=255)                                                                                           agTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑AAGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTaa                                                            >  2:244270/1‑149 (MQ=255)                                                                                            gTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTGGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCAGAAGACATGAATGTGTTATTTCTTGAGGTAAt                                                           >  2:411727/1‑149 (MQ=255)                                                                                              tCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTTCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAAttt                                                         <  2:428898/149‑1 (MQ=255)                                                                                              tCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAAttt                                                         <  2:718281/149‑1 (MQ=255)                                                                                                cGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCa                                                       >  1:204076/1‑149 (MQ=255)                                                                                                     gCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTTTTTTTTTTTTTGATAACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGCCTGCGTTATTTACTCAGGTAATTTCAATGCg                                                  >  2:677405/1‑149 (MQ=255)                                                                                                            tGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTTTTTTTTTTGTTGATTACATTGCATAAATATCCTTGTCTCCTG‑GCGCTATATAAAAAACTGAAGACATTCATGCGTTATTTACTCCGGTAATTTAAATGCGttcatat                                           >  2:367452/1‑144 (MQ=255)                                                                                                               tATGGGCGGTTAAATAAGTAATCCGGGTTCATTATTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACACAGGTAATTTCAATGCGTTAaacgaaa                                        >  1:590527/1‑149 (MQ=255)                                                                                                                       gTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCCTCAATTTCAACCTCTCCGGAACGCT‑GATAAAAAGCTGACGCCATGGACGGGTCCGGTAATCAGCCAATTGCAATGCGTTAAAAGAAAGCTGGCaa                                >  1:354552/1‑149 (MQ=255)                                                                                                                       gTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATCTCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCaa                                >  1:685402/1‑149 (MQ=255)                                                                                                                       gTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATTCGTTATTTACTCAGGTAATTTCAATGCATTAAAAGAAAGCTGGCaa                                >  2:301378/1‑149 (MQ=255)                                                                                                                       gTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGCTAAAAGAAAGCTGGCaa                                >  1:125378/1‑149 (MQ=255)                                                                                                                       gTTAAATAAGTAATCCGGGTTCATTTTTTTACAACTGGATTTGATTACATTGCATAAATATTCGTATACCCAA‑AAGCTATATGAAAACCGGAAGACATTAATGCGCTATTTACTCAGGTTATTTCAATCTGTTAAAAGACAGCTGGCaa                                >  2:318104/1‑149 (MQ=255)                                                                                                                        ttAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAAt                               <  1:342955/149‑1 (MQ=255)                                                                                                                          aaaTAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACGTTGCATAAATATCCCTGTCTCCCT‑ACGCTCTCTAAACACCTGAAGCCATGCATGCGTCATTTACTCACGTCATTTCAATGCGATAAACACAAGCTGCAAATca                             >  2:178227/1‑148 (MQ=255)                                                                                                                            aTAAGTAATCCGGGTTCATTTTTTTTTATTTTTTGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATGCaa                           >  2:636927/1‑149 (MQ=255)                                                                                                                            aTAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCaa                           <  2:124387/149‑1 (MQ=255)                                                                                                                              aaGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAAtt                         <  2:518520/149‑1 (MQ=255)                                                                                                                                   aTCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAg                    <  1:188171/149‑1 (MQ=255)                                                                                                                                              tttttttGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGGAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCAAATTGCAAGCTTAAGACGaa         >  2:453951/1‑149 (MQ=255)                                                                                                                                               ttttttTCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGgaa        >  2:286451/1‑149 (MQ=255)                                                                                                                                                  tttGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACaa     >  2:419121/1‑149 (MQ=255)                                                                                                                                                     gCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCCGGTACAGCAATTGCCAGCTTAAGTCGAAACAAGga  <  1:177669/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                      GGCAAATTAGCCATTTCAAACATTATCATGGCTGATATTTTCCGTAGTCAGGTTTAATGTTTTAAAAGTGCTGTGGGAAAGTGAACAAAGAGTTCCGTAAGCGTTGATGCTATGGGCGGTTAAATAAGTAATCCGGGTTCATTTTTTTGCAACTGGCGTTGATTACATTGCATAAATATCCGTGTCTCCAG‑ACGCTATATAAAAACCTGAAGACATGAATGCGTTATTTACTCAGGTAATTTCAATGCGTTAAAAGAAAGCTGGCAATCCAATTGCCAGCTTAAGTCGAAACAAGGA  >  NC_000913/3657733‑3658029

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑