Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	42.4%	41.4 / 12.1	33	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (14/5);  new base T (0/14);  total (14/19)
Fisher's exact test for biased strand distribution p-value = 1.45e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAT  >  NC_000913/357727‑358000                                                                                                                                                      |                                                                                                                                tGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                               >  2:668159/1‑151 (MQ=255)  gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                              >  1:132596/1‑151 (MQ=255)  gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAtt                                                                                                                               <  1:211968/150‑1 (MQ=255)   aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                             <  1:194112/151‑1 (MQ=255)       cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                         >  2:229829/1‑151 (MQ=255)         tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTTTGCCAGCTATTTTTccgcc                                                                                                                       >  2:359110/1‑151 (MQ=255)                  tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑aaa                                                                                                              <  2:639455/150‑1 (MQ=255)                   aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAc                                                                                                            >  1:352699/1‑151 (MQ=255)                      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgc                                                                                                         <  2:28351/151‑1 (MQ=255)                      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGCGATTCATTTCCGCAAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAAccgc                                                                                                         >  2:201639/1‑151 (MQ=255)                            gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTtc                                                                                                    >  2:73675/1‑150 (MQ=255)                               tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGTCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGAtctctc                                                                                                >  2:409593/1‑151 (MQ=255)                                   gCAATTCAAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCagt                                                                                            >  2:407856/1‑151 (MQ=255)                                    cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCagt                                                                                            >  2:18290/1‑150 (MQ=255)                                                         ggcacggtctcccGTGATTCATCCCCCCCAACACCCGCCTATTTTCCCACCGCCAGGTGCAAAACGGCTTC‑CGGGGCGCCTGTCGGCAAGTTTTTTTCCCGCCCAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAg                                                                     <  2:585305/140‑1 (MQ=255)                                                           cAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAG‑gaaaaaat                                                                   >  1:626449/1‑146 (MQ=255)                                                            ggCGGCAACCGTAATTCATTCCCCCCACCACCCCCTCTTTCATCCCCCGCCGTGTTAAAAAATGCGTC‑CGCGGCGCCTGTCTCCCA‑TTTTTTTTCCCCCCAAACAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCtt                                                                  <  2:458505/150‑1 (MQ=255)                                                             gCGGCTCCGGTGTTTCTTTCCCGCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAAGGCCTT‑CGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCt                                                                   <  1:621502/149‑1 (MQ=255)                                                               ggCTCCCGTGTTTCTTTCCCCCCAACACCCGCGCATTTACCCACCCCCATGTAAAAAAATCCCTT‑CGGGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑aa                                                                         <  1:313683/141‑1 (MQ=255)                                                               ggCTCCCGTGATTCTTTCCCGCCAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCttt                                                                 <  1:611007/149‑1 (MQ=255)                                                                         aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAG‑aaaaaagttttaac                                                             >  1:799094/1‑132 (MQ=25)                                                                              ttccccccaccaCCCGCGCTTTTACCAACCCCCTTGTAAAAAAAGGCCTC‑CGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCAtgtt                                                   <  1:784427/142‑1 (MQ=255)                                                                              ttcccGCCAACACCCGCGATTTTCCCCAACGCCATGGAAAAAAATGCCTG‑CGGGGGGGTTTCCGCCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc                                                        <  2:526978/140‑1 (MQ=255)                                                                                      aacaccCGCTCTTTTCCCCAACGCCATGTAAAAAAATGCCTC‑GGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCAAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                        <  2:440972/151‑1 (MQ=255)                                                                                        caacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑GAAAAAATTTTAACCCGTCATGTTTTGTggggat                                         >  1:541427/1‑144 (MQ=25)                                                                                           ccccgcTTTTACCCACCGCTTTGTGAAAAAATGCCTG‑CGCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCGAAAC‑AAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                    <  2:771707/147‑1 (MQ=255)                                                                                           ccccgcTTTTACCCACCCCCAGGT‑CAAAAAAGCCTTCCGGGGGGGCTGCCTGCCGGTTTTTTTCCCGCCACAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                     <  2:736871/146‑1 (MQ=255)                                                                                           ccGCGCTTTTCCCCACCCCCTTGTGAAAAAATCCTTC‑CGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                     <  1:350740/149‑1 (MQ=255)                                                                                                             cctggtaaaaaaaGGCCTC‑CGGGGGGGCTGCCGGCAATTTTTTTTCCCGCCGAAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                 <  2:795735/143‑1 (MQ=255)                                                                                                              attggcaaaaaaTGCCTT‑GGGGGGGGTTGTCTGCAGGTTTTTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                    <  1:402524/140‑1 (MQ=255)                                                                                                                tgtgCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAACTTTAA‑CCCGCCCAGTTTTGTGGGCATTGCCTCTGGTGAAAAAATGGAAAggg               >  1:614400/1‑150 (MQ=255)                                                                                                                 ttgaaaaatTGCCTG‑CGGGGCGGCTGTCTGCCAGCTTTTTTTCCCCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa              <  1:233969/146‑1 (MQ=255)                                                                                                                               tgcgggggggcTTTCTCCCAGCTATTTTCCCGCCGCAAA‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAt  <  1:622457/141‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                TGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑CGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAAC‑AAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAAT  >  NC_000913/357727‑358000

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: ‑