Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,231,104	0	C	A	42.0%	65.9 / 24.8	50	A739A (GCC→GCA)	ygjK	alpha‑glucosidase
Reads supporting (aligned to +/- strand):  ref base C (22/7);  new base A (0/21);  total (22/28)
Fisher's exact test for biased strand distribution p-value = 2.63e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACCAATCCGGCTTTTGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTGCAACTGC  >  NC_000913/3230962‑3231250                                                                                                                                                 |                                                                                                                                                    tAACCAATCCGGCTTTTGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑t                                                                                                                                             <  2:76468/150‑1 (MQ=255)    ccAATCCGGCTTTTGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAAc                                                                                                                                         >  1:206676/1‑151 (MQ=255)        tCCGGCTTTTGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAAccgcc                                                                                                                                     >  2:531659/1‑151 (MQ=255)         ccGGCTTTTGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAAccgc                                                                                                                                      <  1:838139/149‑1 (MQ=255)                 tGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGAcc                                                                                                                             >  2:65221/1‑150 (MQ=255)                     gcTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTc                                                                                                                        >  2:34600/1‑151 (MQ=255)                            tctgcgggggggggCGTGTGGGGGTGGTTCGTTTCT‑GTTTTGTTTGAAAGGGGAGGGGGCTTTAGGTTTAGGGGGATGATCCCGTGAAGGTGGCGTATACTTTCTCCCGCCA‑C‑CCAAAGGGTTTAACCGCCGATGGACCAATTCAGGaaa                                                                                                                  <  1:517678/139‑1 (MQ=255)                              tagggggggggggGCGTGGGGGGGGATCAGTTTTGGTTGGGTCGGAAG‑GGGAGGGAGCTTTAGGTTTACCGTGAGGAGGCCCGGAGGCGGGGGGATACTTTCTCCCGGCA‑CGCAAAAGGT‑TTAACCGCCGATGGACCAATTCAGGaa                                                                                                                   <  1:250663/138‑1 (MQ=255)                                     gggggggggTAGGGGTGGATCAGTTTTGGTTGGTTCTGAAG‑GGGTGGGGGGGTTACGGTTATCGTAATGATCCCCTAAAGCTGGCGGATCCGTTTTTCCGGCA‑CGCAAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAAcc                                                                                                         <  2:797968/142‑1 (MQ=255)                                     gggggCGCGTAGGGGTGGATCAGTTCTGTTTTGGTCTGAAA‑GGGAGGGAGCGTTCCGTTTATCGTGATGATGCCCTAAAGCGGGCGGATCCGTTCTTCCGGCA‑CGCAAAGGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAAccc                                                                                                        <  2:884465/149‑1 (MQ=255)                                     gTGGGCGTGTGGGGGTGGATCTGTTCTGGTTGGGTCGGAAG‑GGGAGGGGCCGTGACGGTTACCGTGTGGAGCCCCTGAAGCGGGGGGATCCTTTCTCCGGGCA‑CCCAAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAAcc                                                                                                         <  1:586688/150‑1 (MQ=255)                                     gTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAAccc                                                                                                        >  2:112858/1‑151 (MQ=255)                                     gTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAAccc                                                                                                        >  1:917229/1‑151 (MQ=255)                                           gcgTATGGGAGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGAc                                                                                                  >  1:622057/1‑151 (MQ=255)                                            cgTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGAc                                                                                                  >  1:313948/1‑150 (MQ=255)                                              tATGGTTGGATCAGTTCTGTTTGGTTCTAAAG‑GGGATGGGGCGTTCCGTTTGTCGTGAGGATCCCCGGAGGCTGGGGAATACTTTCTCCCGGCC‑CGCAAAAGGT‑TAAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACa                                                                                                 <  1:191381/149‑1 (MQ=255)                                                 gggTGGATCAGTTTTGGTTTGGTCTAAAG‑GGGAGGGAGCTTTACGTTTATCGTGATGATGCCCTGAAGCTGGCGGTTCCTTTTTCCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAg                                                                                                <  2:933460/147‑1 (MQ=255)                                                     gtacctgTTCTGTTTTGGTCTAAAA‑GGGATGGAGCTTTAGGGTTATCGTGAGGATTCCCTAAAGCGGGCGGATTCGTTC‑TCCGGCACCGCAAAAGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAg                                                                                        <  2:832190/145‑1 (MQ=255)                                                         cAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCa                                                                                      >  1:745447/1‑149 (MQ=255)                                                                     ggTCTGAAA‑GGGATGGAGCTTTGCGTTTATCGGAATGAGGCCCTGAGGCGGGGGGATACTTTCTCCCGGCC‑CGCCAAGGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAAt                                                                         <  1:246749/150‑1 (MQ=255)                                                                       tCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTtc                                                                      >  1:53934/1‑151 (MQ=255)                                                                         tGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTtctc                                                                    >  2:290916/1‑151 (MQ=255)                                                                             a‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTgg                                                                >  1:360873/1‑151 (MQ=255)                                                                               ggggTGGGGCTTGACGTTTTTCGTGATGACGCCCTGGAGGTGGCGGATACTTTCTCCCGGCC‑CGCCAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTg                                                                 <  1:615882/149‑1 (MQ=255)                                                                               gggagggaGCGTTACGGTTATCGGGGTGATCCCTAGAACGGGGCGGATCCGTTCTCCGGGCC‑CGCAAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTgg                                                                <  2:887370/150‑1 (MQ=255)                                                                               gggAGGGGGCGTTACGTTTATCGTGATGATGCCCGAAGGGTGGCGGATACTTTCTCCGGGCC‑CGCAAAGGGG‑TAAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTcc                                                                   <  1:356485/147‑1 (MQ=255)                                                                                  aTGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTg                                                            >  1:820398/1‑151 (MQ=255)                                                                                    ggggCGTTACGTTTATCGTGATGATGCCCTGAAGCGGGCGGATACTTTCTCCCGGCA‑CGCAAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTg                                                            <  2:291688/146‑1 (MQ=255)                                                                                     gAGGGTTGCGGTTATGGTGATGATGCCCTGAGGCGGGCGGATACGTTCTTCCGGCA‑CGCAAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCcg                                                         <  2:737502/151‑1 (MQ=255)                                                                                            aCGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCAttt                                                  >  1:846395/1‑151 (MQ=255)                                                                                            aCGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCAttt                                                  >  1:217794/1‑151 (MQ=255)                                                                                              gtttAGCGTGCTGATGCCCTGAAGCTGGCGAAAACTTTCTTCCGACA‑CGCAAAAGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCAtt                                                   <  2:420435/146‑1 (MQ=255)                                                                                                 tATGGTGATGATGCCCTGAAGCTGGGGGATACGTTCTCCCGGCA‑CGCAAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGtat                                              <  2:683765/150‑1 (MQ=255)                                                                                                      tgatgaTGCCCTGAGGCGGGCGGATCCTTTCTCCCGCCA‑CGCCAAGGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATAtg                                           <  1:551066/148‑1 (MQ=255)                                                                                                         tgatgCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGtat                                     >  1:949351/1‑151 (MQ=255)                                                                                                          gatgCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGtat                                     >  1:77886/1‑150 (MQ=255)                                                                                                           atgCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGtata                                    >  1:135507/1‑150 (MQ=255)                                                                                                              cccGGAGGCGGGCGGATCCTTTCTCCCGGCC‑CCCAAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGa                                <  1:480877/151‑1 (MQ=255)                                                                                                               ctaacaGCGGGGGGATATGTTCTTCCGGCA‑CGAAAAGGGG‑TAAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACg                                 <  1:866962/144‑1 (MQ=255)                                                                                                                  gaggcgggCGGATTCGTTCTCCCGGCA‑CGCAAAGGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGAtttt                            <  1:208957/145‑1 (MQ=255)                                                                                                                   aaGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGAttttt                           >  1:702157/1‑151 (MQ=255)                                                                                                                        gggggATACTTTCTTCCGGCA‑CGCAAAAGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGAt                               <  2:462285/139‑1 (MQ=255)                                                                                                                        ggCGGTTACTTTCTCCCGGCA‑CACAAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCg                       <  1:847485/150‑1 (MQ=255)                                                                                                                           ggATACGTTCTCCCGGCA‑CGCAAAAGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAg                   <  2:877133/151‑1 (MQ=255)                                                                                                                                    cttcCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAAttt          >  2:621240/1‑151 (MQ=255)                                                                                                                                      tgcgggacgtacAAAGGT‑TAAGCCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCaataat            <  2:224120/137‑1 (MQ=255)                                                                                                                                       ccGGCA‑CGCAAAGGGT‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTg         <  1:924500/149‑1 (MQ=255)                                                                                                                                       ccGGCA‑CGCAAAAGGG‑TAAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTg         <  2:139732/149‑1 (MQ=255)                                                                                                                                         gccA‑CGCAAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTGCaa      <  2:471482/148‑1 (MQ=255)                                                                                                                                          gCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTGCAAct    >  2:594563/1‑151 (MQ=255)                                                                                                                                            a‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTGCAActgc  >  2:879122/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                    TAACCAATCCGGCTTTTGGCGCTGATATCTACTGGCGTGGGCGCGTATGGGTGGATCAGTTCTGGTTTGGTCTGAAA‑GGGATGGAGCGTTACGGTTATCGTGATGATGCCCTGAAGCTGGCGGATACGTTCTTCCGGCA‑CGCCAAAGGG‑TTAACCGCCGATGGACCAATTCAGGAAAATTACAACCCGCTGACAGGCGCACAGCAAGGCGCACCAAATTTCTCCTGGAGTGCCGCGCATTTGTATATGTTGTATAACGATTTTTTCCGTAAGCAATAATTTGCAACTGC  >  NC_000913/3230962‑3231250

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑