Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,285,853	0	G	T	41.2%	55.2 / 16.6	34	A126S (GCC→TCC)	agaD	N‑acetylgalactosamine‑specific enzyme IID component of PTS
Reads supporting (aligned to +/- strand):  ref base G (2/18);  new base T (14/0);  total (16/18)
Fisher's exact test for biased strand distribution p-value = 8.62e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTGCCCG  >  NC_000913/3285721‑3286001                                                                                                                                          |                                                                                                                                                      gaagaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTC‑TC‑C‑TTATTTTTCCAC‑CCGGGGAAActg                                                                                                                                      >  1:268271/1‑148 (MQ=255)   agaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTC‑TC‑A‑TCA‑TTTTCCCGCCCGGGGAAAccgc                                                                                                                                     >  2:303394/1‑147 (MQ=255)    gaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTgg                                                                                                                                 <  2:663785/151‑1 (MQ=255)    gaaAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTgg                                                                                                                                 <  2:326901/151‑1 (MQ=255)         aGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCg                                                                                                                            <  2:234721/151‑1 (MQ=255)               aaaCCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTT‑TC‑A‑TTA‑TTTTTCCG‑CCAGGGGAACCTGCTGGGGGCg                                                                                                                            >  2:132543/1‑145 (MQ=255)                aaCCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTAt                                                                                                                     <  1:354102/151‑1 (MQ=255)                  ccGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTC‑TC‑A‑TCA‑TTTTCCAG‑CCAGGGGAAACCGCTGGGGGCGGtttttttt                                                                                                                   >  2:579939/1‑151 (MQ=255)                  ccGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTAttt                                                                                                                   <  1:452515/151‑1 (MQ=255)                          ccATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGt                                                                                                           <  1:405687/151‑1 (MQ=255)                               aaaGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTAcc                                                                                                      <  2:65195/151‑1 (MQ=255)                                aaGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGCTTT‑T‑TTT‑TTTTCTAC‑CCTGGGAAA‑CAGCTGGGGCCGCTTTTAATTTTTTCCGttttt                                                                                                       >  1:481827/1‑147 (MQ=255)                                 aGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGCGGGGAGTTTGT‑TC‑‑‑TCC‑TTTTCCAG‑CCCGGGGAAACCGCTGGGGCCGGTTCTATTTTTTGCCGtttttc                                                                                                      >  2:149953/1‑146 (MQ=255)                                    ccTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTTC‑TC‑A‑TCA‑TTTTCCAG‑CCAGGGGAAACTGCTGGGGCCGATTCTTTTTTTTGCCGTTTACCTCCtt                                                                                                 >  2:648873/1‑151 (MQ=255)                                                 cTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTg                                                                                     <  1:149932/150‑1 (MQ=255)                                                       ggCCCACGCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCg                                                                              <  1:259287/151‑1 (MQ=255)                                                        gCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGGTTTTG‑TCTT‑TCT‑TTTTCCGC‑CCGGGGAAACC‑CCCGGGGGCGGTTCTTTTTTTTTCCGCTTTTCCGCTTTTCtttttt                                                                                        >  1:235660/1‑139 (MQ=255)                                                             aTCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTGT‑TT‑ATTCT‑TTTTCCA‑‑CCCGGGGAACCTCCTGGGGCCGGTTTTTTTTTTTTCCCTTTTCCTCCTTTTTTTTTTTCTTCCCGTCGGGTggg                                                                        >  1:180143/1‑150 (MQ=255)                                                             aTCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTGT‑TC‑A‑TCA‑TTTTTCAA‑CCAGGGGAAACTACTCGGGGCGGTTTTTTTTTTTTTCGTTTTCCTTCTTATTTTTTTTCTTCGCGGCGGCTgg                                                                         >  1:584158/1‑150 (MQ=255)                                                                gCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGAccc                                                                     <  2:504205/151‑1 (MQ=255)                                                                     gATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTC‑TC‑C‑TCA‑TTTTCCCG‑CCCGGGGAACCTTCTGGGGGCGGGTTTTTTTTTTTCCCTTTACCTTCTTTTTTTTTTTCTTCGCGGCGGCTGGGCCCCCggc                                                                >  2:654993/1‑149 (MQ=255)                                                                       ttGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGAATTGT‑TC‑T‑TTA‑TTTTTCCC‑CCAGGGGAAACTTCTGGGGCCGGGTTTTTTTTTTTCCCTTTTTCTTCTTTTCTTTTTTTTTCGCGTCGGCTGGGcccccctc                                                                >  1:67312/1‑144 (MQ=255)                                                                           cgatgcgatTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTT‑TC‑C‑TCA‑TTTTCCAG‑CCAGGGGAAACTGCTGGGGGCGATTCTTTTTTTTTCCCTTTTCCTGCTTTTTTTTTTTCTTCGCGTCGGCTGGACCCACCTCGGtt                                                            >  2:465515/1‑149 (MQ=255)                                                                                      tCTGGTTTACTTTGTTGCCGATTATGGC‑GGGGATTTTT‑TC‑C‑TCC‑TTTTTCAA‑CCCGGGGAAACCGCTGGGGGCGATTCTTTTTTTTGCCGTTTTCCTGCTTTTTTTTTTTTTGCGCGTCGGCTGGGCCCAcggcgggttttttatcgg                                                  >  1:498378/1‑136 (MQ=255)                                                                                      tCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCg                                                <  1:206072/150‑1 (MQ=255)                                                                                                   gttgCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGcgatcgat                                  <  1:427327/151‑1 (MQ=255)                                                                                                      gCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATaaa                               <  2:362926/151‑1 (MQ=255)                                                                                                        cGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGt                             <  2:689329/151‑1 (MQ=255)                                                                                                              tGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCg                          >  2:178520/1‑148 (MQ=255)                                                                                                               ggC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCgaga                       <  2:618035/150‑1 (MQ=255)                                                                                                                gC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCgagaga                     <  2:257062/151‑1 (MQ=255)                                                                                                                 c‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGaa                    <  1:410786/151‑1 (MQ=255)                                                                                                                     gAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTc                 <  1:207803/151‑1 (MQ=255)                                                                                                                                        ttGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTGCCCg  >  1:116180/1‑151 (MQ=255)                                                                                                                                          |                                                                                                                                                      GAAGAAAAAGGAGAAAACCGCGACACCATTAAAGGCCTCAAAGTGGCACTGTTTGGCCCAATCGCCGGGATTGGCGATGCGATTTTCTGGTTTACTTTGTTGCCGATTATGGC‑GGGAATTTGC‑TC‑A‑TCA‑TTTGCCAG‑CCAGGGAAACCTGCTGGGGCCGATTCTATTTTTCGCCGTTTACCTGCTTATCTTTTTCCTGCGCGTCGGCTGGACCCACGTCGGTTATTCAGTCGGCGTGAAGGCGATCGATAAAGTGCGAGAGAACTCGCAGATGATTGCCCG  >  NC_000913/3285721‑3286001

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: ‑