Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,247,651	G→T	7.8%	intergenic (‑275/+45)	treA ← / ← dhaM	periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,247,651	0	G	T	7.8%	200.5 / 3.5	59	intergenic (‑275/+45)	treA/dhaM	periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components
Reads supporting (aligned to +/- strand):  ref base G (24/30);  new base T (2/3);  total (26/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCCTGCTGGCAAATCCAGC  >  NC_000913/1247508‑1247793                                                                                                                                                |                                                                                                                                               aaGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTaa                                                                                                                                             <  5:300591/147‑1 (MQ=255) aaGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCACCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTaa                                                                                                                                             <  3:133400/147‑1 (MQ=255)     gATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGc                                                                                                                                        <  8:29471/148‑1 (MQ=255)     gATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGc                                                                                                                                        >  4:68392/1‑148 (MQ=255)     gATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGc                                                                                                                                        <  2:188437/148‑1 (MQ=255)         aataaCGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGa                                                                                                                                    <  5:162839/148‑1 (MQ=255)             aCGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGAc                                                                                                                                <  4:200986/148‑1 (MQ=255)             aCGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGAc                                                                                                                                <  2:51711/148‑1 (MQ=255)                gCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATc                                                                                                                             <  5:275522/148‑1 (MQ=255)                gCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATc                                                                                                                             <  2:90177/148‑1 (MQ=255)                   aaaTAGAGTGATCAAATAACTTCTGTTTATTATCCAGCCAGAGGCGTTGTGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGa                                                                                                                          <  3:9319/148‑1 (MQ=255)                        gagTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGAt                                                                                                                     <  5:91601/148‑1 (MQ=255)                              tCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATc                                                                                                               >  2:180977/1‑148 (MQ=255)                                 aaTAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTTGTGAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACCTCAGACCGATGCCATCCGa                                                                                                            >  6:96401/1‑148 (MQ=255)                                  aTAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGaa                                                                                                           <  3:68392/148‑1 (MQ=255)                                  aTAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGaa                                                                                                           >  6:224260/1‑148 (MQ=255)                                   tAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAAc                                                                                                          <  1:97899/148‑1 (MQ=255)                                     aCGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACa                                                                                                         <  5:406/147‑1 (MQ=255)                                                       gccagcGGCGGTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGt                                                                                      >  6:169684/1‑148 (MQ=255)                                                        ccagcGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGtt                                                                                     >  7:145802/1‑148 (MQ=255)                                                         cagcGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAGACCATTAGTGCTCAGTAAATAGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGCCGGtt                                                                                     >  8:300796/1‑147 (MQ=255)                                                                  tGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGc                                                                           >  5:271467/1‑148 (MQ=255)                                                                    ggTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGt                                                                         >  8:265640/1‑148 (MQ=255)                                                                     gTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGa                                                                                                            >  2:252519/1‑112 (MQ=255)                                                                     gTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGa                                                                                                            <  1:252519/112‑1 (MQ=255)                                                                         gTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGAc                                                                                                                                <  6:24114/88‑1 (MQ=255)                                                                         gTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGAc                                                                                                                                >  5:24114/1‑88 (MQ=255)                                                                         gTGATTAGCGAAGAAAAATCATCATAAATTGGGGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTa                                                                     <  2:43310/147‑1 (MQ=255)                                                                           gATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACg                                                                  >  2:191348/1‑148 (MQ=255)                                                                            aTTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGt                                                                 >  4:287536/1‑148 (MQ=255)                                                                                gCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGTTAGTTAAAAACCATTAGTGCTGATTAAATTGCCGTATGACATCAGAACGATGACATCCGAACAGTGGCTTAACACTGACGTTTGAAACGTTGCGTTTTAACTTCCat                                                             >  8:13778/1‑147 (MQ=255)                                                                                gCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGATTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACACTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCag                                                             >  8:8866/1‑148 (MQ=255)                                                                                 cGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCagc                                                            <  7:265640/148‑1 (MQ=255)                                                                                        aaaTCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCagcgttagcg                                                     <  5:172358/148‑1 (MQ=255)                                                                                         aaTCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACg                                                                                                                       >  8:160759/1‑81 (MQ=255)                                                                                         aaTCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACg                                                                                                                       <  7:160759/81‑1 (MQ=255)                                                                                           tcatcaTAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGttt                                                  <  8:133522/148‑1 (MQ=255)                                                                                                atAAATTGGTTAAAAATATAACATGTAGTTAAAAACAATTAGTGATGATTAAATTGACGGCTTAAATCAGAACGATGCCATCCGTACAGTGGCTTAACCCAGCCGGTTGAAACGTTGCTTTTTAACGTCCAGCGTTAGCGTTtcttct                                             <  5:96401/148‑1 (MQ=255)                                                                                                  aaaTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTgg                                           >  2:165338/1‑148 (MQ=255)                                                                                                   aaTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGATTAAATTGCCGGATGACATCAGAACGATGCCATCCTAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGt                                          <  7:13778/148‑1 (MQ=255)                                                                                                   aaTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGATTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGt                                          <  7:8866/148‑1 (MQ=255)                                                                                                   aaTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGt                                          <  6:271467/148‑1 (MQ=255)                                                                                                    aTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGtt                                         >  4:24266/1‑148 (MQ=255)                                                                                                         tGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATc                                    <  5:224260/148‑1 (MQ=255)                                                                                                                tataACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGTAACGTTGCGTTTTTTCGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACa                             <  1:165338/148‑1 (MQ=255)                                                                                                                       ggTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTtctc                      <  5:169684/148‑1 (MQ=255)                                                                                                                           gTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCAcc                   <  3:287536/147‑1 (MQ=255)                                                                                                                             tAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGc                                  >  3:175310/1‑130 (MQ=255)                                                                                                                             tAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGc                                  <  4:175310/130‑1 (MQ=255)                                                                                                                             tAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCctg                >  2:55934/1‑148 (MQ=255)                                                                                                                              aaaaaCCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCctgc               >  4:223202/1‑148 (MQ=255)                                                                                                                                     aTTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCt                                                                                                   >  2:18144/1‑57 (MQ=255)                                                                                                                                     aTTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCt                                                                                                   <  1:18144/57‑1 (MQ=255)                                                                                                                                      ttAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCCTGCTGGCAAAt       >  2:207910/1‑148 (MQ=255)                                                                                                                                           gCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGt                           >  2:238950/1‑123 (MQ=255)                                                                                                                                           gCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGt                           <  1:238950/123‑1 (MQ=255)                                                                                                                                           gCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCCTGCTGGCAAATCCAGc  >  7:239666/1‑148 (MQ=255)                                                                                                                                             tGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCCTGCTGGCAAATCCAg   >  2:269102/1‑145 (MQ=255)                                                                                                                                             tGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCCTGCTGGCAAATCCAg   <  1:269102/145‑1 (MQ=255)                                                                                                                                                |                                                                                                                                               AAGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTATCGCATACAGTTTCTCACCCTGCTGGCAAATCCAGC  >  NC_000913/1247508‑1247793

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑