Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,163,377	0	G	T	43.8%	29.6 / 16.9	32	E40* (GAA→TAA)	thiK	thiamine kinase
Reads supporting (aligned to +/- strand):  ref base G (3/15);  new base T (14/0);  total (17/15)
Fisher's exact test for biased strand distribution p-value = 1.47e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCG  >  NC_000913/1163228‑1163527                                                                                                                                                      |                                                                                                                                                        gCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGa                                                                                                                                                        <  2:390735/151‑1 (MQ=255)       gggCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCa                                                                                                                                                  <  1:380202/151‑1 (MQ=255)        ggCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAg                                                                                                                                                 <  1:329077/151‑1 (MQ=255)           gAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGTTTTTTCCTTTAACATCAgg                                                                                                                                                >  2:391757/1‑149 (MQ=255)                 aTCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCATTTaaaaacaagg                                                                                                                                               >  1:699130/1‑136 (MQ=255)                   cTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGGTTTTCCTTGAAAATCATGGGCAGCGgtt                                                                                                                                      >  1:158443/1‑151 (MQ=255)                                     cGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCa                                                                                                                    <  1:720048/151‑1 (MQ=255)                                      gTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCTTTTAAAAACAGAGCCAGCGTTTttttgttggggcgccgccc                                                                                                                   >  2:550149/1‑138 (MQ=255)                                          cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCCTTTTAAATCAAGGCCCGCGGTTTTTTTTGTGTCAGCCGCACgcac                                                                                                               >  1:325611/1‑148 (MQ=255)                                          cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATc                                                                                                               <  1:574640/151‑1 (MQ=255)                                          cGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGGTTTTTTATTTAACAACCCGGCCAGGGGGTTTTTTTGCGCCcgccgccc                                                                                                                   >  2:111710/1‑145 (MQ=255)                                             agcaATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTGTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTg                                                                                                            <  2:40920/151‑1 (MQ=255)                                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTTTTTTTACATCAAGGCCAGCCGTTTTTTTTGTGTCAGCCGCACCGTCCTCATg                                                                                                         >  2:362689/1‑151 (MQ=255)                                                aataatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGAt                                                                                                          <  2:323602/150‑1 (MQ=255)                                                   aatCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATgcg                                                                                                       <  2:222176/150‑1 (MQ=255)                                                    atCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTCTTATTTAACATTCAGGCCAGCGGTTTTTTTTTCGTcgggcctccgcacc                                                                                                              >  2:301022/1‑129 (MQ=255)                                                      cccATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTTATTTAAAAACAAGGCCCGCGGTTTTTTTTGTGTCAGCCGCCCGATCCCGATGcgccg‑c                                                                                                  >  1:360610/1‑151 (MQ=255)                                                               cgcgACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGCGGTTTCTCATTGAACATCAACGGCAGCGGTTTGTTTTGGGGCAGCCCACCGATCCCTATGcgccg‑ccg                                                                                                >  2:207646/1‑142 (MQ=255)                                                                  gacgaATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCCTTTTACATTAGGGCCCCCGTTTTTTTTTGGGTCAGCCGCCCGATCCTCGTGCGCCG‑CAGGcccccgt                                                                                        >  1:102719/1‑144 (MQ=255)                                                                             gTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGt                                                                             <  2:622318/149‑1 (MQ=255)                                                                               cgcgCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATc                                                                          <  2:334214/150‑1 (MQ=255)                                                                                 cgcTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCATTTTAAATCAAGTCCAGCGGTTTTTTGTGGGTTAGCCGCCCGATCCTCATGCGCCG‑CCGGCCGCGTTTTTGTGCCCGGATCggg                                                                       >  1:260312/1‑151 (MQ=255)                                                                                           cGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTTCTTTAACAACAGGGCCAGCGGTTTTTTGTTTGTCAGGCGCCCGCTCCCGATGCGCCGCCGGTCCCCG‑TCTTTCGCCCGTAACGGGCttttt                                                                 >  1:690904/1‑145 (MQ=255)                                                                                            gCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGATTTTTTATTTAAAATCAAGGACCGCGTTTTTTTGTGCGGCCGGCGCCCGATTCTTATGGGCCG‑CCGGCCGCCTGTTTGCGCCCGTATCCGGCttttt                                                                 >  2:223672/1‑144 (MQ=255)                                                                                                  tcatcCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGGGGTTTTTCATTTTAAAACAAGGCCACCGGTTTTTTTTTGGTCCGCCGCCCGGTCCTTATGCGCCG‑CCGGCCCCCGTCTTTCGCCCGGATCGGGCTTTTTTCCAAATAccc                                                      >  1:691155/1‑151 (MQ=255)                                                                                                           cACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCAtt                                             <  1:86435/151‑1 (MQ=255)                                                                                                             cgacgTTTAATAGTGGGCTTAGTGGCGGGATTTTTCTCTTTGAGCATCAGGGCCAGCGGTTTGTTGTGCGTCAGCCTCACGGTCCTGATGCGCCG‑CAGTGCGCGTTCTTGCGCCAGTATCGTGCTTTATCACAACTACCCGCATGCAtt                                             <  2:536217/149‑1 (MQ=255)                                                                                                                 gTTTAATAGTGGGCTTAGTGGCGGGAGTTTTTTCTTTTAAAATCCAGGCCCGCGGTTTGTTGTGGGGGCGCCGCCCGGACCTTGAGGGCCG‑CCGGCCCCGTTCCTGGGCCCGGATTGGGGGTTTTCATAACCACCCccatgcgatggcc                                         >  1:421224/1‑142 (MQ=255)                                                                                                                           gggCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCAt                              <  1:732306/150‑1 (MQ=255)                                                                                                                                   tGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATAtctc                     >  1:115152/1‑151 (MQ=255)                                                                                                                                     gCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCg                   <  1:61336/151‑1 (MQ=255)                                                                                                                                       gggAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTg                 <  2:574298/151‑1 (MQ=255)                                                                                                                                                      gAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCg  <  1:546571/151‑1 (MQ=255)                                                                                                                                                      gAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCg  <  2:541089/151‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                        GCAGACGGGCGAAATTATCTGGTCAGGTAAAGGTGCCGTTTCGCAGCAATAATCCCATCACGCGCGACGAATTGCTGTCGCGCTTTTTCCCGCAGTATCATCCCGTCACGACGTTTAATAGTGGGCTTAGTGGCGGGAGTTTTCTCATTGAACATCAGGGCCAGCGTTTTGTTGTGCGTCAGCCGCACGATCCTGATGCGCCG‑CAGTCCGCGTTCTTGCGCCAGTATCGGGCTTTATCACAACTACCCGCATGCATTGCACCGAAGCCGCATTTATATCTCCGTGACTGGATGGTAGTCG  >  NC_000913/1163228‑1163527

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑