Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,361,439	C→T	13.8%	A89V (GCA→GTA)	gltF →	periplasmic protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,361,439	0	C	T	13.8%	69.6 / 5.9	29	A89V (GCA→GTA)	gltF	periplasmic protein
Reads supporting (aligned to +/- strand):  ref base C (16/9);  new base T (2/2);  total (18/11)
Fisher's exact test for biased strand distribution p-value = 6.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.82e-01

GTTCATATGTTTTTCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGACCACTGGTCAGCAGCGACCCCCACATGGAAAGCCT  >  NC_000913/3361168‑3361726                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                                gTTCATATGTTTTTCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAAtt                                                                                                                                                                                                                                                                                    >  1:533414/1‑285 (MQ=255)  ttCATATGTTTTTCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGt                                                                                                                                                                                                                                                                               <  2:533414/289‑1 (MQ=255)      tatGTTTTTCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAAc                                                                                                                                                                                                                                                                            >  2:95284/1‑288 (MQ=255)            tttCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAg                                                                                                                                                                                                                                                                     >  2:253577/1‑289 (MQ=255)            tttCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAg                                                                                                                                                                                                                                                                     >  1:239221/1‑289 (MQ=255)                                           tgtgCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTaa                                                                                                                                                                                                                                      <  1:95284/289‑1 (MQ=255)                                                                        tGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTAt                                                                                                                                                                                                         >  2:488478/1‑289 (MQ=255)                                                                                                             tcattgggCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGAATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCt                                                                                                                                                                    <  2:10287/283‑1 (MQ=255)                                                                                                               catcGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGc                                                                                                                                                                                                             >  2:89094/1‑246 (MQ=255)                                                                                                               catcGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGc                                                                                                                                                                                                             <  1:89094/246‑1 (MQ=255)                                                                                                               catcGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGaaa                                                                                                                                                                           <  2:389410/280‑1 (MQ=255)                                                                                                               catcGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGaaa                                                                                                                                                                           >  1:389410/1‑280 (MQ=255)                                                                                                                                   gTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGAc                                                                                                                                                                                                                                                    <  1:534985/187‑1 (MQ=255)                                                                                                                                   gTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGAc                                                                                                                                                                                                                                                    >  2:534985/1‑187 (MQ=255)                                                                                                                                   gTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAACAGACACATCCTATATTGAAAAATCTTATGATACTCTCGTAGCTATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCCCCTaa                                                                                                                                              >  2:193510/1‑289 (MQ=255)                                                                                                                                   gTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTaa                                                                                                                                              >  1:193830/1‑289 (MQ=255)                                                                                                                                        tGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGTACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGAc                                                                                                                                         >  2:220513/1‑289 (MQ=255)                                                                                                                                        tGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGAc                                                                                                                                         >  2:89865/1‑289 (MQ=255)                                                                                                                                                    gttACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGgc                                                                                                                              >  1:252215/1‑288 (MQ=255)                                                                                                                                                              gcggcATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGTACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCa                                                                                                                    <  1:220513/288‑1 (MQ=255)                                                                                                                                                                                                tGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCAcgcg                                                                                 >  1:380560/1‑289 (MQ=255)                                                                                                                                                                                                     tGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGa                                                                            <  2:239221/289‑1 (MQ=255)                                                                                                                                                                                                          ccGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATa                                                                       <  1:253577/289‑1 (MQ=255)                                                                                                                                                                                                                                           ggCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACt                                       <  1:488478/288‑1 (MQ=255)                                                                                                                                                                                                                                             ccGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGa                                     >  2:327603/1‑288 (MQ=255)                                                                                                                                                                                                                                                                      aCCTGCACAGTACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGAc                                    <  1:53536/264‑1 (MQ=255)                                                                                                                                                                                                                                                                      aCCTGCACAGTACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGAc                                    >  2:53536/1‑264 (MQ=255)                                                                                                                                                                                                                                                                           cacaGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCCGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAgg                                                                                                                                                          >  1:474313/1‑141 (MQ=255)                                                                                                                                                                                                                                                                           cacaGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGACCACTGGTCAGCAGCGACCCCCACATGGaaa      >  2:551614/1‑289 (MQ=255)                                                                                                                                                                                                                                                                                cACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGACCACTGGTCAGCAGCGACCCCCACATGGAAAGCCt  >  2:13584/1‑288 (MQ=255)                                                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                                                                GTTCATATGTTTTTCAAAAAGAACCTCACAACAGCTGCTATTTGTGCAGCACTTTCTGTTGCAGCATTCAGTGCCATGGCAACAGATTCAACTGATACAGAATTAACTATCATCGGCGAGTATACCCCTGGTGCATGTACCCCAGTTGTTACGGGCGGCGGCATTGTTGACTATGGGAAACATCATAACAGTGCGCTGAATCCGACCGGTAAAAGTAATAAACTGGTTCAACTGGGCCGCAAAAACAGCACATTAAATATAACCTGCACAGCACCAACGCTAATTGCTGTAACCTCCAAGGATAACCGTCAGTCGACCATTGTAGCGTTAAACGACACATCCTATATTGAAAAAGCTTATGATACTCTCGTAGATATGAAGGGAACGAAAAACGCCTTTGGTTTAGGTTCTGCGCCTAATGGACAAAAAATTGGCGCTGCATCCATTGGTATTGACAGGTCTAATGGTGGGATTCACGCGGCGGACGATACAGGTGAAATTCCTGTCGACCTGATTCAAACTGACCACTGGTCAGCAGCGACCCCCACATGGAAAGCCT  >  NC_000913/3361168‑3361726

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑