Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	328,791	0	A	G	54.0%	20.4 / 50.2	37	S182P (TCC→CCC)	betI	choline‑inducible betIBA‑betT divergent operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base A (1/16);  new base G (20/0);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 1.32e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.58e-07

GGCCGGGTTAATGGTCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGC  >  NC_000913/328644‑328940                                                                                                                                                    |                                                                                                                                                            ggCCGGGTTAATGGTCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑t                                                                                                                                                         <  1:754722/150‑1 (MQ=255)  gCCGGGTTAATGGTCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTa                                                                                                                                                       <  2:272492/151‑1 (MQ=255)             ggTCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGGCGGGGGA‑‑TTA‑GCGg‑ggg                                                                                                                                              >  2:654410/1‑147 (MQ=255)                         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)                                                                                                                                                    |                                                                                                                                                            GGCCGGGTTAATGGTCTCGAAGGTGCGACCGCTGGTGGCGGAGGTATAACCACCATGTATATAAAGCTGCTGTTCTGCCATTCGGGACATCACGTCTCCTCGGTTAATCGGTGGGTAGATGCTGAGTGATAAAGTGGCGGGTCAGGGAA‑‑TTA‑GCGC‑GGGTTTTATC‑CAGC‑GGTTTGCCGCTCAGAGCCGCGCGCAGCCATAATCCATCAATCAGCGCGGCCAGGCCGTAGCCCGCTTCCTGTGCCTGTTCGCGCGGCAATTCGCGACGAAACTCGCTCACCAGATTCGACAGCAAGC  >  NC_000913/328644‑328940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑