Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,475,493	T→C	F19F (TTT→TTC)	yjgL →	protein YjgL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,475,493	0	T	C	97.0%	117.8 / ‑3.6	33	F19F (TTT→TTC)	yjgL	protein YjgL
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (14/18);  total (15/18)
Fisher's exact test for biased strand distribution p-value = 4.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.05e-01

CGCAGTGGGCGCGCCAGCCCAGGTTCGCAAAGCAGTAGTGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCATATTAAGTCCTCATCTTATTCTAAAGATACTAATGGCAATGAA  >  NC_000913/4475257‑4475730                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                               cgcAGTGGGCGCGCCAGCCCAGGTTCGCAAAGCAGTAGTGAAGATGCTGATGGCGTGCTGACTTTTCGCCGTAAATAAATCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCATAGACGTTCTTATTCACTCAAGGAGTTCGGCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAggg                                                                                                                                                                                                                                  >  1:52298/1‑248 (MQ=255)                aGCCCAGGTTCGCAAAGCAGTAGTGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTg                                                                                                                                                                                                                  <  2:345817/251‑1 (MQ=255)                 gCCCAGGTTCGCAAAGCAGTAGTGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTgg                                                                                                                                                                                                                 >  1:91573/1‑251 (MQ=255)                  cccAGGTTCGCAAAGCAGTAGTGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGc                                                                                                                                                                                                                <  2:196812/251‑1 (MQ=255)                     aGGTTCGCAAAGCAGTAGGGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTGACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTGAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATGATTCTCAACATATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCgtg                                                                                                                                                                                                             <  2:30817/251‑1 (MQ=255)                                gCAGTAGTGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGgaatgaat                                                                                                                                                                                                  <  1:328316/251‑1 (MQ=255)                                      gtGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGAtttt                                                                                                                                                                                            <  2:301922/251‑1 (MQ=255)                                                 gATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTg                                                                                                                                                                                  <  1:91195/250‑1 (MQ=255)                                                      cGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCgggg                                                                                                                                                                            >  1:356556/1‑251 (MQ=255)                                                          atgaCTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCa                                                                                                                                                                        <  1:11221/251‑1 (MQ=255)                                                           tgaCTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGc                                                                                                                                                                         >  2:306008/1‑249 (MQ=255)                                                                tttCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGAt                                                                                                                                                                    <  2:277927/249‑1 (MQ=255)                                                                               cTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATAttct                                                                                                                                                   >  1:284879/1‑251 (MQ=255)                                                                                    ggTTTACGGCGCGTTTGTGAAAAGCGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTtctc                                                                                                                                              >  2:38059/1‑251 (MQ=255)                                                                                          cGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAg                                                                                                                                        <  1:255449/251‑1 (MQ=255)                                                                                             cGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCAt                                                                                                                                     <  1:125907/251‑1 (MQ=255)                                                                                              gAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCAtt                                                                                                                                    >  2:122647/1‑251 (MQ=255)                                                                                                                         atTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTAc                                                                                                         <  1:184872/251‑1 (MQ=255)                                                                                                                               ttGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTgg                                                                                                    <  2:52298/250‑1 (MQ=255)                                                                                                                                tgtgAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGt                                                                                                  >  2:24969/1‑251 (MQ=255)                                                                                                                                           tttGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTagag                                                                                                                             <  1:11988/213‑1 (MQ=255)                                                                                                                                           tttGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTagag                                                                                                                             >  2:11988/1‑213 (MQ=255)                                                                                                                                                           gTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAAc                                                                       <  1:290964/251‑1 (MQ=255)                                                                                                                                                             tCTTATTCGCTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACg                                                                      >  2:39724/1‑250 (MQ=255)                                                                                                                                                                 aTTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCg                                                                 <  1:224578/251‑1 (MQ=255)                                                                                                                                                                        cAAGGAGTTCGTCATGAGCAAAATAGCAGATTTAAATTATTCTCAACACATTACAGTAGCCGACAATTTCAAACAA‑AAAAGTTAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTGTTTGGCAAAGATATTTACCCTGGGTGATGTGGATTGTAGCAAACGCTCCAACGAAGCGGGTAg                                                            <  2:46423/249‑1 (MQ=255)                                                                                                                                                                                        aGCAAAATATCAGATTTAAATTATTCTCAACACATTACATCAGACGA‑AACTTTCAACAACAAACGTGAAATTTTAAATACCAGACGTGTTGGCATGAATGATTTTGCCAGTATTGCCGGGAGGAAGGATAACAGAAGGAATATTCTTTCTCCTGGAGAATTTTTAGAGTTTTTGGCAAAGATATTTACACTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCatat                                          >  1:370554/1‑251 (MQ=255)                                                                                                                                                                                                     aTTTAAATTATTCTCAACACATTACATTAGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCATATTAAGTCCTCATCt                             >  1:357223/1‑251 (MQ=255)                                                                                                                                                                                                             tattCTCAACACATTACATTAGCCGACAATTTCAAACAC‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCATATTAAGTCCTCATCTTATTCTa                      >  1:285399/1‑250 (MQ=255)                                                                                                                                                                                                                          ttacattaGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTag                                                                                                                               >  1:176892/1‑132 (MQ=255)                                                                                                                                                                                                                          ttacattaGCCGACAATTTCAAACAA‑AAAAGTGAAGTTGTAAATACCTGGCGTGTGGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCGCCTGGAGCATTTTTag                                                                                                                               <  2:176892/132‑1 (MQ=255)                                                                                                                                                                                                                              attaGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCATATTAAGTCCTCATCTTATTCTAAAGATACTAATGGCAATg    >  1:68207/1‑251 (MQ=255)                                                                                                                                                                                                                                 aGCCGACAATTTCAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCATATTAAGTCCTCATCTTATTCTAAAGATACTAATGGCAATGaa  <  1:208029/250‑1 (MQ=255)                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                               CGCAGTGGGCGCGCCAGCCCAGGTTCGCAAAGCAGTAGTGAAGATGCTGATGGCGTGATGACTTTTCGCCGTAAATAACTCAAGGTTTACGGCGAGTTTGTGAAAAGAGCGTTTTTTGATATTTTTTTGTGAGTAAAATTTGTAATGCTTAGACGTTCTTATTCACTCAAGGAGTTCGTCATGAGCAAAATATCAGATTTAAATTATTCTCAACACATTACATTAGCCGACAATTTTAAACAA‑AAAAGTGAAGTTTTAAATACCTGGCGTGTTGGAATGAATGATTTTGCCCGTATTGCCGGGGGGCAGGATAACAGAAGGAATATTCTTTCTCCTGGAGCATTTTTAGAGTTTTTGGCAAAGATATTTACCCTGGGTTATGTGGATTTTAGCAAACGCTCCAACGAAGCGGGTAGAAATATGATGGCTCATATTAAGTCCTCATCTTATTCTAAAGATACTAATGGCAATGAA  >  NC_000913/4475257‑4475730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑