Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,604,344	0	C	T	46.0%	31.6 / 15.6	38	S62F (TCT→TTT)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (5/15);  new base T (17/0);  total (23/15)
Fisher's exact test for biased strand distribution p-value = 3.12e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGG  >  NC_000913/4604201‑4604494                                                                                                                                                |                                                                                                                                                       aGAAACATGCGTCATGAGTAGGATCGGAATTGAGAGTTTATTCTGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACTAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTCGCGGCGGTCGctttttcttttttt                                                                                                                                                 >  2:843982/1‑149 (MQ=255) aGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTttttctttttct                                                                                                                                                 <  2:1042834/151‑1 (MQ=255)     aaaTGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCa                                                                                                                                             <  1:1066170/151‑1 (MQ=255)           gTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCactag                                                                                                                                         >  2:47747/1‑145 (MQ=255)           gTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGaa                                                                                                                                       <  1:124536/151‑1 (MQ=255)             cATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCCATTTTTTTTTTTATGACAt                                                                                                                                            >  1:490155/1‑144 (MQ=255)                 agtagtATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAgc                                                                                                                                 <  1:882423/151‑1 (MQ=255)                    agtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTTATTTTTTTTTTTTCTTGCATGGGGAGGGAgcg                                                                                                                                >  2:264869/1‑149 (MQ=255)                    agtaTCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAgcg                                                                                                                                >  1:455457/1‑149 (MQ=255)                            tATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGTGAAGTGAGCGCAGAGAggg                                                                                                                       >  1:782889/1‑150 (MQ=255)                             aTTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGGGCAGAGAggg                                                                                                                       >  1:432561/1‑149 (MQ=255)                             aTTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGa                                                                                                                      <  2:592794/150‑1 (MQ=255)                              ttGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGAtt                                                                                                                    >  1:681369/1‑151 (MQ=255)                                gagaGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTAt                                                                                                                  >  1:945976/1‑151 (MQ=255)                                           cAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCctgact                                                                                                       <  1:194267/151‑1 (MQ=255)                                             gAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGGAGTGAGCGGAGGGAGGGGTTTTCTTGCctggc                                                                                                        >  2:336726/1‑146 (MQ=255)                                             gAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTATGCGGTCTTCTGTTTTTAAAATTTTTCCCTTAGAAGTGAGCGCAGAGGGGGGTTAACTTgtc                                                                                                            >  1:1054687/1‑142 (MQ=255)                                                 gTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTTCCCTGCGGAGAGAGCGCACAGAGGGAGTTTTTTGCCTGTCTTaaat                                                                                                  >  2:522966/1‑148 (MQ=255)                                                  tttGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGTGAAGTGATCGGAGAGAGGGATTATCtttctttagtgcact                                                                                                  >  2:29202/1‑136 (MQ=255)                                                    tGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCCGAGAGGGGTTTTCTTGCCCGACTGAACTGGCg                                                                                              >  1:484830/1‑151 (MQ=255)                                                        ggTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGCAGAGGGCGCAGGGGGGGGTTATCTTGCCTGACTGAACTGGCGAtt                                                                                           >  2:830917/1‑150 (MQ=255)                                                        ggTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTa                                                                                          <  2:398700/151‑1 (MQ=255)                                                                 tataAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAggg                                                                                                                       <  1:100442/113‑1 (MQ=255)                                                                    aaGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGt                                                                               <  1:75470/150‑1 (MQ=255)                                                                             aCCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCAATTTTTTTTTTTTTTCCATTAGGAATGAGCGGCGAGGGGGGTTTTTTTTCCTGTCTGGACTGGCGATTAAGTTTTCCCGTACCCGGCggt                                                                     >  2:382169/1‑149 (MQ=255)                                                                                    ccAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTTGTTAt                                                              >  1:155095/1‑151 (MQ=255)                                                                                       gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGAGAGGGCAGAGGGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCCCGTAACCGGCGTTTAGTTAt                                                              >  2:1066216/1‑148 (MQ=255)                                                                                       gTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGATGTTAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGc                                                           <  2:271668/151‑1 (MQ=255)                                                                                             aGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGgatga                                                     <  1:892148/151‑1 (MQ=255)                                                                                                cATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTTGTTATTTCgg                                                         >  1:850899/1‑144 (MQ=255)                                                                                                    tCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGGCATTTTTTTTTTTTCTGCCATGAGAAGAGAGCGCAGAGAGGGATTATTTTTTCTGTCTGAACTGGGGGTTAAGTTTTCGCGGACCCCGCGTTTTGTTTTTTGGGGTGGTGAAAtt                                              >  2:613041/1‑151 (MQ=255)                                                                                                     cAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATAtt                                              <  2:58076/150‑1 (MQ=255)                                                                                                          tGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGGTGATGATATTGaa                                           >  1:1020244/1‑148 (MQ=255)                                                                                                                   gcgGATCTCGTTTGCGGCGGTCATTTTTTTTTTTTTTGCCATGAGAAGGGAGCGCAGAGAGGGGTTATCTTGCCTTACTGAACTGGCGGTTAAGGTTTCGCGTACCCGGCGGTTTGTTTTTGCGGGTGATGATATTTAAGCTCGGCTGGtt                               >  2:387231/1‑151 (MQ=255)                                                                                                                          tcGTTTGCGGCGGTCATTTTTTTTTTTTCTGCCATGAGAAGTGAGGGCCGAGAGGGGTTATCTTGCCTGACTGAACTGGCGATTAAGGTTTCGCGGACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGGTcct                        >  1:148421/1‑149 (MQ=255)                                                                                                                            gTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTg                      <  1:944195/151‑1 (MQ=255)                                                                                                                                gcggcgGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCg                   <  1:957658/150‑1 (MQ=255)                                                                                                                                     ggTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCa             <  1:1054160/151‑1 (MQ=255)                                                                                                                                         aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGc         >  1:186540/1‑151 (MQ=255)                                                                                                                                         aTTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCAGCAcc           <  2:1034897/149‑1 (MQ=255)                                                                                                                                            ttttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTgg      >  1:1023703/1‑151 (MQ=255)                                                                                                                                              ttctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGa     <  1:130057/150‑1 (MQ=255)                                                                                                                                               tctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACg   >  1:845342/1‑151 (MQ=255)                                                                                                                                                ctttttctGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACgg  >  1:598161/1‑151 (MQ=255)                                                                                                                                                |                                                                                                                                                       AGAAAAATGCGTCATGAGTAGTATCGGTATTGAGAGTTTATTCAGAAAGTTTGCGGGTAACCCTTATAAGCTCCATACCTATACCAGTCAGGAGTCATTTCAGGATGCCATGTCGCGGATCTCGTTTGCGGCGGTCATTTTTTCTTTTTCTGCCATGAGAAGTGAGCGCAGAGAGGGATTATCTTGCCTGACTGAACTGGCGATTAAGTTTCCGCGTACCCGGCGTTTAGTTATTGCGGATGATGATATTGAAGCTCGGCTGATTGGTTCATTGTCGCCATCACCGCTGGACGG  >  NC_000913/4604201‑4604494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑