Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,465,787	0	G	A	40.0%	42.9 / 15.8	41	R132C (CGC→TGC)	treB	trehalose‑specific PTS enzyme: IIB and IIC component
Reads supporting (aligned to +/- strand):  ref base G (19/5);  new base A (0/16);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 3.39e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTGCTCTTTATCAACCTGC  >  NC_000913/4465643‑4465923                                                                                                                                                  |                                                                                                                                           ccGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAAcc                                                                                                                                      <  2:520248/151‑1 (MQ=255) ccGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAAcc                                                                                                                                      >  1:437302/1‑151 (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)                                                                                                             ggacggttcccaaggggAAAACCGCCAACAACATGGCAAAAACG‑GAGGAAAAAC‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCtttt                          <  1:526459/136‑1 (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)                                                                                                                                 aTCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTGCTCTTTATCAAcc     >  2:620028/1‑151 (MQ=255)                                                                                                                                 aTCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTGCTCTTTATCAAcc     >  1:370819/1‑151 (MQ=255)                                                                                                                                    gCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTGCTCTTTATCAACCTgc  >  2:60428/1‑151 (MQ=255)                                                                                                                                                  |                                                                                                                                           CCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGTAGATCGTTTGCAGGGAAGGGTACATTTG‑CGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCACATTGCGAAAACC‑GAGGATCAAA‑CCGCCGCTAATCAACGCGGGCAGCAACGGGAAGAAGATCACCGCGAAATGAGAGATCAACTGCTCATGCCATTTCATATTATGCCGGGCGGCTTTTTTTACCTGCTCTTTATCAACCTGC  >  NC_000913/4465643‑4465923

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑