Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	328,807	0	A	T	48.6%	18.2 / 27.5	37	D176E (GAT→GAA)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (4/15);  new base T (18/0);  total (22/15)
Fisher's exact test for biased strand distribution p-value = 5.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGGCTGCTG  >  NC_000913/328668‑328951                                                                                                                                                |                                                                                                                                                   gCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GTGTTTTATC‑CAGC‑GGtt                                                                                                                                        <  2:1465/150‑1 (MQ=255)   gACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCTGGGGA‑‑ATA‑GGGG‑GGGGTTTTTT‑CAGC‑GGgtt                                                                                                                                       >  1:443023/1‑149 (MQ=255)   gACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑ATA‑GCGC‑GGGGTTTTTT‑CCGC‑GGgtt                                                                                                                                       >  1:281489/1‑149 (MQ=255)       gCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑TTA‑GGGCGGGGTTTTTTC‑CACG‑GGtt                                                                                                                                        >  1:398093/1‑145 (MQ=255)             ggCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGc                                                                                                                           <  1:129037/151‑1 (MQ=255)              gCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGTAGGGGA‑‑ATT‑GCGC‑GGGGTTTTTT‑CAGCGGGTTTGcgccccaagcc                                                                                                                           >  1:830026/1‑141 (MQ=255)                  aGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGGAGGGGA‑‑TTA‑GCGC‑GGGGGTTTTT‑CAAC‑GGGTTGCCGCTCCGAGCcgc                                                                                                                        >  1:63616/1‑149 (MQ=255)                   ggTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGTGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCcgcgcg                                                                                                                     <  1:44033/151‑1 (MQ=255)                      ataACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGATGTTA‑GTG‑‑GGGTTTTTTC‑TA‑C‑GGTTTGCCGCCCAGAACcgc                                                                                                                        >  1:245681/1‑145 (MQ=255)                           caccaTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGGA‑‑ATA‑GCGG‑GGGGGTTTTT‑CAGC‑GGGTTTTCGCCCCGAACCGCGCgccgcc                                                                                                                >  1:841933/1‑148 (MQ=255)                            accaTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGGG‑‑ATA‑AAGG‑GGGGGTTTTT‑CAAC‑GGGTTGTCGCCCCCAGCCGCGCGCGGcc                                                                                                                >  1:562634/1‑147 (MQ=255)                             ccaTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAAt                                                                                                           <  1:103168/151‑1 (MQ=255)                              caTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑TTA‑GAGCGGGGGTTTTTC‑CGCC‑GGTTTG‑CGCCCCGAGCCGCGCGCAGccccaa                                                                                                            >  1:386852/1‑145 (MQ=255)                               aTGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGGAGGGGG‑‑TTAGGGGG‑GGGTTTTTTT‑CA‑C‑GGGTTGCCGCTCCCAGCCgcgcgccaccccaatac                                                                                                         >  2:837657/1‑140 (MQ=255)                                 gTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑ATA‑AAGC‑GGGGGTTTTT‑CCGC‑GGGTTGCCGCCCAGAGCCGCGCGCGGCCATa                                                                                                             >  1:303287/1‑145 (MQ=255)                                  tatataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑ATA‑ACGG‑GGGGTTTATT‑CAGC‑GGGTTGTCGCTCCGAACCGCGCGCAGCCCTaa                                                                                                            >  1:648543/1‑145 (MQ=255)                                     ataAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCGGGGGA‑‑ATA‑GCGC‑GGGGGTTTTT‑CCGC‑GGGTTGGCGCTCCGAGGCGCGCGGCGCCaccaatccccaa                                                                                                    >  2:824716/1‑139 (MQ=255)                                              ctgTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCACGGGA‑‑ATA‑GAGC‑GGGGTTTTTT‑CATC‑CGTGTTGAGCTCAGAGCCGCCCGCGCCCCTAAATCatcaacaacagc                                                                                             >  2:624589/1‑141 (MQ=255)                                                gTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGGGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGcc                                                                                         <  2:734511/150‑1 (MQ=255)                                                gTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCa                                                                                        <  2:715830/151‑1 (MQ=255)                                                           cGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGGA‑‑TTA‑GCGG‑GGGGGTTTTT‑CCGC‑GGGTTTTCGCCCCGAGGCCCGCGCGCCCCTAATCCCACCATCAACGCGGGCCGGCCGGAGgcc                                                                             >  1:852498/1‑151 (MQ=255)                                                                     cGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGTGCAGGGGA‑‑TTA‑GGGG‑GGGGGTTTTCTCGGC‑GGTTT‑TCGCCCCGAAGCGCGCGGCGCCCCAATCCTCCTAACATCGCGGCCAGGCCGCAGTCCCCTccc                                                                       >  2:847161/1‑147 (MQ=255)                                                                           ctcGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑ATA‑GGGC‑GGGGTTTTTT‑CAAC‑GGGTTTTCGCTCCCAGCCCCGCGCCGCCATAAACCCTCAAAAAACGCGGCCCGGCCCTAGCCCCCCTcc                                                                       >  1:415697/1‑141 (MQ=255)                                                                                    tCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGGA‑‑ATA‑GCGC‑GGGGTTTTTT‑CCGC‑GGGTTTGCGCCCCGAGCCGCGCGCCGCCACAATCCCTCAAACAACGCGGCCCGGCCGCAGCCCCCCTCCTTTGCCCGTTCGCGCgg                                                      >  1:732253/1‑149 (MQ=255)                                                                                     cGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGc                                                     <  1:401111/149‑1 (MQ=255)                                                                                           gTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGGGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTcgcg                                             <  1:254708/151‑1 (MQ=255)                                                                                             aGATGCTGAGTGATAAAGTGGCGGGGCAGGGGA‑‑ATA‑GCGC‑GGGGTTTTTT‑CAGC‑GGGTTGCCGCCCACAGCCGCGCGCCGCCCCAATCCATCAATCAGCGCGGCCCGGCCCGAGCCCGCCTCCCTTGCCTGGTTGCGCGGCAATATGcgac                                           >  1:360714/1‑151 (MQ=255)                                                                                                        gaaaaaGGGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTGGCCGCGCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCt                                 <  2:404082/147‑1 (MQ=255)                                                                                                              gTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGa                          <  2:442915/151‑1 (MQ=255)                                                                                                                   gggTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGa                     <  1:490214/151‑1 (MQ=255)                                                                                                                    ggTCGGGGAA‑‑TTA‑GCGC‑GGGTTTTACC‑CAGC‑GGTTTGCCGCTCAGGCCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGAc                    <  2:160505/151‑1 (MQ=255)                                                                                                                       cAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGc                 >  2:839578/1‑151 (MQ=255)                                                                                                                         gggAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGc                 <  1:374247/149‑1 (MQ=255)                                                                                                                           gAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAgc             <  1:619455/151‑1 (MQ=255)                                                                                                                                  a‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCCATCAGCGCGCCCAGGCCGTAGCCAGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGCTTCGACAGCAAgcggcg         >  2:643840/1‑150 (MQ=255)                                                                                                                                      gc‑gGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGgct      <  1:440147/150‑1 (MQ=255)                                                                                                                                           gTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGGctgctg  >  1:147769/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                   GCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGCGGCGGCTGCTG  >  NC_000913/328668‑328951

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑