Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	48.1%	15.5 / 13.2	28	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (3/11);  new base T (13/0);  total (17/11)
Fisher's exact test for biased strand distribution p-value = 3.39e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAC  >  NC_000913/4604195‑4604492                                                                                                                                                        |                                                                                                                                                     aCTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATtttttct                                                                                                                                                     <  2:280994/151‑1 (MQ=255)    cATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATtttttcttt                                                                                                                                                   <  1:623018/150‑1 (MQ=255)          aaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCAtttttttttttttttcc                                                                                                                                            >  1:331242/1‑146 (MQ=255)          aaaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTTcc                                                                                                                                            >  1:540557/1‑151 (MQ=255)                      gggtagtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGa                                                                                                                                 <  1:574296/148‑1 (MQ=255)                      gAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGCGAAGTg                                                                                                                                  >  2:574284/1‑149 (MQ=255)                       agtagtATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                                                                                               <  1:517782/151‑1 (MQ=255)                         tagtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTTTGCCATTAGAAGGGAg                                                                                                                                >  1:538787/1‑148 (MQ=255)                             aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCagag                                                                                                                         <  1:142969/151‑1 (MQ=255)                             aTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGACATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCaggg                                                                                                                         >  1:537082/1‑149 (MQ=255)                                    ttGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTGTAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTTTGCCCTGCGAAGTGAGCGCGGGGAGGGAtt                                                                                                                  >  1:202800/1‑151 (MQ=255)                                         agTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGTTTATCtt                                                                                                             <  2:474145/151‑1 (MQ=255)                                           tttATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGTTCTTTTTTTATTTTTCTTCCAGGAGAAGTGGGCGGCGAGGGGGGTTAtagtt                                                                                                            >  1:607135/1‑146 (MQ=255)                                           ttattccggAAAGTTT‑CGGGTTACCCTTTTAAGGTTCCATA‑CTATTCCCAGCCGGGGTTATTTCCGGGAGCCATTTTGGCGGTCTTCTTTTGC‑GCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCt                                                                                                              <  1:611604/139‑1 (MQ=255)                                                     aaGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCCTTTTTTTTTTTTCTGCCCTGAGAAGTGAGCGCAGAGGGGGGTTATCTTTCCTGACTGaa                                                                                                  >  2:379102/1‑150 (MQ=255)                                                       gTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAATGAGCGCAGGGAGGGGTTATCTTGCCTGACTGaa                                                                                                  >  2:457918/1‑148 (MQ=255)                                                        tttGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTTTCCTGTGAAGTGAGCGCAGAGAGGGATTATTTTTTCCGTCTGAACttg                                                                                              >  2:481078/1‑149 (MQ=255)                                                             gggTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGAtt                                                                                         <  2:567789/151‑1 (MQ=255)                                                                tAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTTTCTTTCCTGACTGGAATGGCGGtt                                                                                         >  2:423934/1‑148 (MQ=255)                                                                 aaCCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGGTTTCTTTCCTGACTGAAATGGGGAtt                                                                                         >  2:39544/1‑147 (MQ=255)                                                                                        ataCCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTa                                                                 <  1:379109/149‑1 (MQ=255)                                                                                        ataCCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAg                                                                <  1:162822/150‑1 (MQ=255)                                                                                                cAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGGGAAGGGAGCGCAGAGAGGGATTATCTTTCCTGACTGAACTGGCGATTAAGTTTTCGCGTACCCGGCGGTTAGTTATTGCgg                                                       >  2:270761/1‑151 (MQ=255)                                                                                                 aGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTTAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCgg                                                       >  1:615788/1‑150 (MQ=255)                                                                                                  ggAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgat                                                     <  1:198217/151‑1 (MQ=255)                                                                                                   gAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatg                                                    <  1:463911/151‑1 (MQ=255)                                                                                                      tCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGGTTTGTTATTGCGggtg                                                    >  1:569421/1‑148 (MQ=255)                                                                                                          ttCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGGTTAAGGTTTCGCGTACCCGGCGGTTAGTTATTGCGGATGATGatat                                             >  2:176071/1‑151 (MQ=255)                                                                                                                          cgcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGGGGAGTGAGGGCAGGGAGGGGTTTTCTTGCCTTACTGAACTGGCGGTTAAGTTTCCGCGTACCCGGCGTTTAGTTTTTGCGGATGATTATATTTAAGCTCGGCTGAt                              >  2:161301/1‑151 (MQ=255)                                                                                                                                   cGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCa                       <  2:27498/149‑1 (MQ=255)                                                                                                                                            cggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATc            >  2:119675/1‑151 (MQ=255)                                                                                                                                                      ttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAc  >  2:309592/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                     ACTCATAGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAA‑GCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCA‑TGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGAC  >  NC_000913/4604195‑4604492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑