Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,371	0	C	T	43.2%	43.4 / 29.1	44	L38F (CTC→TTC)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base C (2/23);  new base T (19/0);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.49e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGG  >  NC_000913/1163225‑1163521                                                                                                                                                     |                                                                                                                                                        ggTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCAt                                                                                                                                                     <  1:134484/151‑1 (MQ=255)    gCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGa                                                                                                                                                  <  1:416667/151‑1 (MQ=255)    gCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGa                                                                                                                                                  <  2:394358/151‑1 (MQ=255)    gCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGa                                                                                                                                                  <  1:489425/151‑1 (MQ=255)     cAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGaa                                                                                                                                                 <  1:404168/151‑1 (MQ=255)          gggCGAAATTATCTGGTCAGGTAAATGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTTGC‑GGGA‑GTTTTCTCATTGAACAT‑Ca                                                                                                                                           <  2:761204/151‑1 (MQ=255)          gggCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GTTTTTTCttt                                                                                                                                                    >  1:108341/1‑143 (MQ=255)            gCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAgg                                                                                                                                         <  1:791135/151‑1 (MQ=255)                 aTTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GTGTTTTCTTTTAAAAT‑Cac                                                                                                                                          >  2:479531/1‑144 (MQ=255)                 aTTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAg                                                                                                                                    <  2:245239/151‑1 (MQ=255)                  ttATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCTTTTTAAAT‑CAAGGcc                                                                                                                                      >  1:270700/1‑148 (MQ=255)                  ttATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCCTTTAACAT‑Caacggc                                                                                                                                      >  2:571896/1‑143 (MQ=255)                   tATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCTTTTTACAT‑CAggg                                                                                                                                        >  2:345269/1‑145 (MQ=255)                           cAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTttgttg                                                                                                                          <  2:590509/151‑1 (MQ=255)                            aGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTTGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTtgttgt                                                                                                                         <  2:841732/151‑1 (MQ=255)                            aGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCTTTTTACAT‑CAGGGGCCGCGGtttttt                                                                                                                           >  1:741190/1‑149 (MQ=255)                             ggTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCTTTTTAAAT‑CAAAGGCAGCGTtttttt                                                                                                                           >  2:564487/1‑148 (MQ=255)                             ggTAAAGGTGCCGTTTCGCAGCAATAAGCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTTGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTtgtg                                                                                                                        <  2:105126/151‑1 (MQ=255)                              gTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCTTTTTACAT‑CCAGGCCAGGGGgttgttt                                                                                                                          >  2:757131/1‑147 (MQ=255)                                 aaGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTTATTGAAAAA‑CAAGGCCCGCGGTTTTTtgtggg                                                                                                                      >  2:358591/1‑147 (MQ=255)                                     tGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTTCTTTAACAA‑CACGGGCACCGGTTTTTTTTGCGTCAGcc                                                                                                                >  1:816194/1‑151 (MQ=255)                                                agcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTg                                                                                                     <  2:360699/151‑1 (MQ=255)                                                     taatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGGGTTTTGTTGTGCGTCAGCCGCCCGATCCTGATgc                                                                                                 <  2:2965/150‑1 (MQ=255)                                                      aatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATgcg                                                                                                <  1:30361/150‑1 (MQ=255)                                                              cACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCATTTAAAAA‑CACAGCCCGCGGTTTTTTGTGGGGGAGCCGCCCGAACCTGATGcgccgccggcc                                                                                       >  2:829650/1‑146 (MQ=255)                                                                     gacgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GTTTTTTTTTTGAACAT‑CCCGGCCAGCGGTTTTTTTTGCGTTAGCCCGCCGCACCTGATTCGCCCCCGTCCGCGtt                                                                                  >  2:382031/1‑149 (MQ=255)                                                                             gCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCa                                                                         <  1:716422/150‑1 (MQ=255)                                                                             gCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCa                                                                         <  2:536257/150‑1 (MQ=255)                                                                                gTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGt                                                                       <  1:338313/149‑1 (MQ=255)                                                                                 tCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GGTTTTTCCTTTAACCT‑CACTGCCAGCGTTTTGTTGTGGGGCAGCCGCACGATCCTGGTGCGCCGCAGTCCCCGCTCTTTCGCCCCTATc                                                                    >  2:778429/1‑151 (MQ=255)                                                                                   gcgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCATTGAAAAT‑CAAGGCCAGCGTTTTTTTGTGGGTCAGCCGCACGATCCTGTTGCGCCGCCGTCCCCGTTCTTGCGCCAGGATCgg                                                                  >  1:715602/1‑151 (MQ=255)                                                                                     gcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGG‑GTTTTTTCTTTTAA‑AT‑CAGGGGCCGCGGTTTTTTTTTGGTTAGCCCCCCCGTCCCGATGCGCCCCCGGCCCCGGTCTTTCGCCCCGATCggg                                                                 >  1:327276/1‑150 (MQ=255)                                                                                       tttttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGG‑GTTTTTTTTTTGTAAAT‑CAGGGCCAGCGGTTTTTTTTGGGGCTGCCCCCCCCTCCTTTTGCGCCGCCGCCCCCGGTCTTGCGCCACGATCggg                                                                 >  2:676069/1‑148 (MQ=255)                                                                                        ttttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCtt                                                              <  2:637040/150‑1 (MQ=255)                                                                                         tttCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCttt                                                             <  1:433809/150‑1 (MQ=255)                                                                                                 aGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGAG‑GATTTCTTATTTAACATCCAGGGCAAG‑GTTTTGTTGTGTGTCGGCCGCACGATCCTGATGCGCCCCAGGCCGCGTTCTTGCGCCCGGATCGGGCTTTTTcac                                                        >  2:191723/1‑147 (MQ=255)                                                                                                  gTATCATCCCGTCACGACGTTTAATAGTGTGCTTAGTGGC‑GGGG‑GGTTTTTTTTTTAAAAA‑CAAGGGCAGCGGTTTTTTTTGGGGTCGCCGCACCAACCCGATGCGCCCCAGCCCCCGGTCTTGCGCCCGGATCGGGCgtttt                                                           >  1:62016/1‑141 (MQ=255)                                                                                                    atcatcCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTAc                                                  <  1:135941/150‑1 (MQ=255)                                                                                                          ccGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCgcatg                                           <  1:440640/151‑1 (MQ=255)                                                                                                               acgacgTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCAtt                                       <  1:682387/150‑1 (MQ=255)                                                                                                                  acgTTTAATAGTGGGCTTAGTGGC‑GGGA‑GGTTTTTCATTTTACAT‑CAAGGCCAGCGGTTTTTTTTGCGTCAGCCGCACGACCCTGATGCGCCGCCGTCCCCGTTCTTGCGCCCCTATCCGGCGTTTTTACCAATACCCCCCTGCATTTCa                                    >  1:665999/1‑150 (MQ=255)                                                                                                                     tttAATAGTGGGCTTAGTGGC‑GGGAGGTTTTTTCTTTTAA‑AT‑CAAGGGCAGGGTTTTGTTGTGGGGCGGCCCCACGACCCCGTTGCGCCGCCGTCCGGGGTCTTTCGTCCGCATTGGGCCTTTTCACAACTCCCCGCACGCACTGCAcc                                  >  2:250541/1‑149 (MQ=255)                                                                                                                                           gggA‑GTTTTCTCATCGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGCTCCTGAGGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACCACCCGCATGCAGTGCACCGACGCCGCATTTATAtctc               >  2:139484/1‑147 (MQ=255)                                                                                                                                                  tttCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTgg      <  1:204990/150‑1 (MQ=255)                                                                                                                                                     ctcATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATgg  >  1:4499/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                        GGTGCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGC‑GGGA‑GTTTTCTCATTGAACAT‑CAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCGCAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGG  >  NC_000913/1163225‑1163521

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑