Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	328,803	0	T	G	64.1%	‑2.1 / 38.2	40	T178P (ACC→CCC)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base T (6/8);  new base G (25/0);  total (32/8)
Fisher's exact test for biased strand distribution p-value = 4.88e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.05e-04

TCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGGCTGCTGA  >  NC_000913/328658‑328952                                                                                                                                                     |                                                                                                                                                      tctcGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGGATTAGCGG‑GGGgttttt                                                                                                                                                  >  1:112559/1‑149 (MQ=255)  ctcGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATc                                                                                                                                                 <  1:331184/151‑1 (MQ=255)        ggTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCC‑GGGGATTAGCGC‑GGGGTTTTTTTAGCgg                                                                                                                                           >  1:154557/1‑151 (MQ=255)         gTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCg                                                                                                                                            <  1:117658/149‑1 (MQ=255)                             ggTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGGATTAGCGC‑GGGGTTTTTTCCGCGGGTTGCCGCCCAGAGCcgcgcg                                                                                                                      >  1:638589/1‑151 (MQ=255)                             ggTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGATTAGAGG‑GGGGGTTTTTTAGCGGGTTGGCGCGCAGAGCcggggg                                                                                                                      >  2:381787/1‑147 (MQ=255)                              gTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGAATAGGGC‑GGGGGTTTTTCAGCGGGTTGCCGCTCAGAGGcgcgcg                                                                                                                      >  1:96671/1‑150 (MQ=255)                              gTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGAATAACGCGGGGGTTTTTCCGCCGGTTT‑TCGCCCCGAGCcgcgcg                                                                                                                      >  1:338550/1‑150 (MQ=255)                                    ccaccaTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCAGGGGAATTGGGGG‑GGGGTTT‑TTCAGCGGGTTTTCGCCCCGAGCCGCGCgccgccc                                                                                                                >  2:408878/1‑149 (MQ=255)                                        caTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATc                                                                                                           <  2:60966/151‑1 (MQ=255)                                           gTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCC‑GGGGAATAGCGC‑GGGGTTTTTTCAGCGGGTTGCCGCCCCGAGCCGCGCGCCGCCAAAATTCat                                                                                                        >  1:502734/1‑151 (MQ=255)                                           gTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGGA‑GGGGACTATCGCGGGGGTTTTTCAACGGGTTTTCCGC‑CACAGCCGCGCGCCGCCATAAACCat                                                                                                        >  1:159741/1‑151 (MQ=255)                                           gTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCAGGGGAATTTCGGG‑GGGGTTTTCCCACCGGTTTG‑CGCTCAGAGACCGGCGCAGccccaaaacaa                                                                                                        >  1:436458/1‑142 (MQ=255)                                           gTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGATTAGCGC‑GGGGGTTTTTCAGCGGTTTTCCGCCCCGAGCCGCGCGCCGCCCTAATCCat                                                                                                        >  1:327071/1‑151 (MQ=255)                                             atataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGGCG‑GGGAATATGGGG‑GGGGTTTTTCC‑CCGGGTTTTCGCCCCGAACCGCGCGCAGCCCTaaatcctc                                                                                                       >  1:572554/1‑144 (MQ=255)                                             atataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGGATTAGCGG‑GGGGTTTTTTTAGCGGGTTTTCGCTCCCAGCCgcgcgcgcgcctaaaccacca                                                                                                      >  2:117826/1‑136 (MQ=255)                                             atataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAAATAGCGC‑GGGGTTTTTTCAGCGGGTTGGCGCTCAGAGCCGCGCGCCGCCACAAACCctca                                                                                                      >  1:283017/1‑151 (MQ=255)                                             atataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCC‑GGGGAATAGCGC‑GGGGTTTTTTCACCCGGTTTTCGCCCCGAGGCGCGCGCCGCCCTAATCCatca                                                                                                      >  1:343604/1‑151 (MQ=255)                                             atataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCC‑GGGGAATAGAGC‑GGGGTTTTTTCAGCCGGTTTTCGCTCAGAGGCGCGCGCCGCCATAAttcctc                                                                                                       >  1:548240/1‑145 (MQ=255)                                             atataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGAATAGCGC‑GGGGTTTTTTCAGCGGGTTTGCGCCCCGAGCCCCGCGCGGccccaaatcctc                                                                                                       >  1:246955/1‑140 (MQ=255)                                                taAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCatcaatc                                                                                                   <  1:132642/151‑1 (MQ=255)                                                        ctgTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGAATATAGC‑GGGGTTTTTTCAGCGGGTTTGCGCTCCCAGGCGCGCGGGGCCCCAAACCAACAAACAACGCggg                                                                                           >  1:223049/1‑150 (MQ=255)                                                           ttCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGctc                                                                                         <  1:163089/150‑3 (MQ=255)                                                                 cATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCC‑GGGGATTAGCGC‑GGGGTTTTTCCCGCCGGTTGCCGCCCAGAGCCGCGCGCCGCCCCAAACCCTCAATCAACGCGGCCAGGCCgc                                                                                   >  2:563538/1‑149 (MQ=255)                                                                  aTTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGAATTGAGG‑GGGGTTTTTCCCACGGGTTGTCCCCCAGAGCCGCGCGCAACCATAATACATCAATCCGCGcggcccggcccccg                                                                                 >  1:261273/1‑147 (MQ=255)                                                                    tCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGcc                                                                               <  2:371123/151‑1 (MQ=255)                                                                    tCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGcc                                                                               <  1:232689/151‑1 (MQ=255)                                                                       ggACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCT‑GGGGATTAGCGC‑GGGGTTTTTTTCGCGGGTTGGCGCTCCGAGCCGCGCGCCGCCACAAACCATCAAACAGCGCGGCCCGGCCGCAGgccc                                                                             >  2:142763/1‑149 (MQ=255)                                                                       ggACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGATA‑GGGGAATAACGCGGGGCTTTTTCCA‑CGGGTTTCCGCCCACAACCGCCCGCCACCACAAATCCCCAATCAGCGCGCCCAGGCCCCAGcccc                                                                             >  1:75237/1‑149 (MQ=255)                                                                        gACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCatc                                                                                                       <  1:454318/123‑1 (MQ=255)                                                                               cGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGGAATAACGC‑GGGGTTTTTTCAGCGGGTTGCCGCCCCGAGCCGCGCGCAGCCCTAATCCCTCAATCAGCGCGGCCCGGCCGGAGCCCCCCTcccttg                                                                    >  1:439557/1‑147 (MQ=255)                                                                                 tctcCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCC‑GGGAATTAGAGG‑GGGGTTTTTTCAGCGGGTTTGCGCCCCGAGCCGCGCGGCGCCCAAAATCATCAAACAACCCGGGCAGGCCCGAGCCCCCCTcccttgc                                                                   >  1:514726/1‑145 (MQ=255)                                                                                  ctcctcGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGATTAGCGC‑GGGGTTTTTTCAGCGGTTTTGCCCTCCGAGCCGCGCGCCGCCACAAACCATCAAACAGCGCGGCCCGGCCCTAACCCGCCTCCTGTGcc                                                                  >  1:52045/1‑150 (MQ=255)                                                                                               cGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCA‑GGGGATTAGAGC‑GGGGGTTATTCCGCGGGTTGGCGCCCAGAGCCGCGCGCCGCCCCAAAACATCAATCACCGCGGCCAGGCCGCAGCCCCCCTCCCGTGCCTGTTCGCGCGGcca                                                    >  2:40761/1‑149 (MQ=255)                                                                                                 gTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGGCC‑GGGGAATAACGCGGGGTTTTTTCCA‑CGGTTTTTCGCCCCCAGGCCCGCGCCGCCCCAAATCCTCAAACAACGCGGCCCCGCCGCAGCCCCCCTCCCCTGCCTCTTCCCGCgggcaat                                                  >  2:641180/1‑146 (MQ=255)                                                                                                        gATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGGTTTTTTCAGCGGTTTTTCGCCCAGAGCCGCGCGCCGCCCTAATACATCAATCAACGCGGCCCGGCCGGAGCCCCCCTCCTGTGCCCGTTTGCGCGGCAATTTCcgacg                                           >  1:346127/1‑151 (MQ=255)                                                                                                                                     gggAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCaa                >  2:156306/1‑151 (MQ=255)                                                                                                                                       gAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAg               >  1:211348/1‑150 (MQ=255)                                                                                                                                                   ggTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGgctg      >  2:266489/1‑148 (MQ=255)                                                                                                                                                   ggTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGgctg      >  2:291976/1‑148 (MQ=255)                                                                                                                                                    gTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGGCTGCTGa  >  1:247590/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                      TCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGC‑GGGTCA‑GGGAATTAGCGC‑GGGTTTTATCCAGCGGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGGCTGCTGA  >  NC_000913/328658‑328952

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑