Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,465,763	0	T	G	39.0%	44.0 / 16.8	41	M140L (ATG→CTG)	treB	trehalose‑specific PTS enzyme: IIB and IIC component
Reads supporting (aligned to +/- strand):  ref base T (17/8);  new base G (1/15);  total (18/23)
Fisher's exact test for biased strand distribution p-value = 9.57e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTG  >  NC_000913/4465623‑4465907                                                                                                                                              |                                                                                                                                                   cGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCg                                                                                                                                          <  2:671392/151‑1 (MQ=255)    gccgccCATTATTTTCACCACAGACCACCAAATACCAACCGGCAGGTAGTAGTAGATCTCTTCACCGTTCATCCACAGAAAATCGTAGATCGTTTGCAGGGAACGGTACATTTG‑CCCCAGCTTCTGACCATTGCTCATGGGCAAAt                                                                                                                                            <  1:28512/146‑1 (MQ=255)       gccCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATc                                                                                                                                    >  2:321814/1‑151 (MQ=255)          cATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCCTCACCGATCAACCACAAAAAATCGTAGTTCGTTTGCAGGGAAGGGTACATTTG‑AGCCAGCGCCTTACCGTTGCTCATGGGCAAATCGCCGATcac                                                                                                                                  >  1:530722/1‑150 (MQ=255)                     ccGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAAcc                                                                                                                      >  1:437302/1‑151 (MQ=255)                     ccGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAAcc                                                                                                                      <  2:520248/151‑1 (MQ=255)                          gACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAgg                                                                                                                 >  1:398936/1‑150 (MQ=255)                                 aaaTACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑cc                                                                                                        >  1:189372/1‑151 (MQ=255)                                 aaaTACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑cc                                                                                                        >  2:660125/1‑151 (MQ=255)                                   aTACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑ccgc                                                                                                      >  2:251268/1‑151 (MQ=255)                                      ccgaccgGCAGGGAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑Ccgccgc                                                                                                   >  1:491503/1‑151 (MQ=255)                                          ccgGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTaa                                                                                                >  2:178158/1‑150 (MQ=255)                                           cgGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATc                                                                                              >  1:303834/1‑151 (MQ=255)                                            ggCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATc                                                                                              >  2:321720/1‑150 (MQ=255)                                                       gaagaTCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGgcagc                                                                                  >  2:244330/1‑151 (MQ=255)                                                        aagaTCGCTTCACCGACAACCCACAAAAAATCGTAGGTTGTTTGCAGGAAGGGGTACTTTCG‑CGCCAGCGTCGGCCCGTTGCTCAGGGGAAATGCGCGGACCACA‑TGGGAAAACCGGAGGATAAAA‑CCGCCGCTAATCAACGCGGgcag                                                                                   <  1:492767/149‑1 (MQ=255)                                                          gaccGCTCCACCGACCACCCAAAAAAAAGCGTAGTTCTTTTGC‑GGGGAGGGTAAAATTGCCGCCAGCGTTGGCCCGTTGCTAAGGGGCAAACCCCGAATCAC‑TTGGCAAAACC‑GGGGAACAAATCCGCCGCTAATCAACGCGGGCAGCaa                                                                                <  1:648185/147‑1 (MQ=255)                                                           aTCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTGGCAGGGAAGGTTACATTGG‑CGCCAGCGTCTGACTTTTGCTCGGGGGCAAACCGCCGATCACATGGGAAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACg                                                                              <  2:622020/151‑1 (MQ=255)                                                           aTCGCTTCACCGATCAACCACAGAAAATCGTAGAGCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCACA‑CCGCCGCTAATCACCGCGGGCAGCAACg                                                                              >  1:544663/1‑151 (MQ=255)                                                                   aCCGAACAACCAAAAAAAACCGTAGATGTTGTGCGGGGAGGGGTACTTGTG‑CGCCAGCGTCGGACCGTTGCTCGGGGCAAAACCGCCGACCACAGTGAGAAAACA‑GAGAACCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGgaagaa                                                                       <  1:60937/150‑1 (MQ=255)                                                                        tCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCAc                                                                 >  1:102911/1‑151 (MQ=255)                                                                          aaCCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACcg                                                               >  2:194134/1‑151 (MQ=255)                                                                              acaGAAAATCGTAGATCGTTTGCGGGGAAGGGTACATTTG‑CGCCAGCGTCTGCCCGTTGCTCATGGGCAAACCGCCGATCACATGGCAAAACCC‑GAGGAAAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGa                                                            <  2:370522/150‑1 (MQ=255)                                                                                   aaaTCGTAGATCGTTTGCAGGGAGGGGTACTTTTG‑CGCCAGCGTCTGACGGTTGCTCAGGGGAAAATCGCGGATCACATTGCAAAAACC‑GAGAATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATgag                                                      <  2:535611/151‑1 (MQ=255)                                                                                      tCGTAGATCGTTTGCGGGGAAGGGTACATTGG‑CGCCAGCGTCTGCCCTTTGCTCATGGGCAAATCGCCGATCAAATTGCAAAACCG‑GAGAATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATgagag                                                    <  2:244255/150‑1 (MQ=255)                                                                                         tAGTTCGTTGGGAGGGAAGGTTACATTGG‑CGCCAGCGTCGGACCGTTGCTCAGGGGCAAACCGCCGATCACTTTGCGAAACCC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGAt                                                  <  1:289701/149‑1 (MQ=255)                                                                                            aTCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACt                                             >  1:597551/1‑151 (MQ=255)                                                                                                tttGCAGGGAAGGGTACATTGG‑CGCCAGCGTCTGCCCGTTGCTCAGGGGCAAATCGCCGATCACATTGCAAAACCC‑GAGAATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTg                                            <  2:422390/148‑1 (MQ=255)                                                                                                      gggAGGGGTACTTTGG‑CCCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCAAAACCC‑GAGAATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCAt                                       <  2:262724/147‑1 (MQ=255)                                                                                                      gggAAGGTTACATTGG‑CGCCAGCGTCTGCCCGTTCCTCAGGGAAAAATCGCCGATCACTTTGCAAAACCC‑GAGGATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCAt                                       <  2:437316/147‑1 (MQ=255)                                                                                                      gggAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAACCGCCGATCACATTGCAAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCa                                        <  2:422162/146‑1 (MQ=255)                                                                                                      ggaaggggTACATTTG‑CGCCAGCGGCTGACCGTGGCTCAGGGGAAAACCGCCGATCGCATAGCAAAAACG‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGc                                     <  2:135391/144‑1 (MQ=255)                                                                                                           ggggACATTTG‑CGCCGGCGTTTCCCCGTTGCTAAGGGAAAAACCGCAAAACGCGTTGGGAAACCG‑GAGTTAAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCa                                   <  2:645254/146‑1 (MQ=255)                                                                                                           gggTACTTGCG‑CGCCAGCGTCTGCCCGTTGCTCAGGGGCAAACCGCCGACCCCATTGCAAAACCC‑GGGGATAAAC‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCa                              <  1:657971/151‑1 (MQ=255)                                                                                                                       ccccAGCGTCTGCCCGTTGCTCAGGGGAAAACCGCCGACCACATTGCAAAACCC‑GAGGATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCgg                   <  2:73443/149‑1 (MQ=255)                                                                                                                          cAGCGTCTGCCCGTTGCTAAGGGGAAAATCGCCGATCACATTGCAAAACCC‑GAGGATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGggcg                <  2:189375/151‑1 (MQ=255)                                                                                                                                    ctgttccgcATGGACAAACCGCCGATCACATGGAAAAACCG‑GAGTATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGggcggc              <  2:210317/135‑1 (MQ=255)                                                                                                                                    ccGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCttttttt       >  1:506492/1‑150 (MQ=255)                                                                                                                                       ttGCTCAGGGACAAATCGCCAATCACATTGCAAAACCC‑GAGGACCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTAc     <  2:35587/149‑1 (MQ=255)                                                                                                                                        ggCTCAGGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTg  >  1:97178/2‑151 (MQ=255)                                                                                                                                          cTCAGGGGAAAATCGCCGATCACATGGCAAAACCC‑GAGGATAAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTg  <  2:647284/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                   CGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTG  >  NC_000913/4465623‑4465907

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑