Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	53.6%	14.2 / 31.4	28	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (10/3);  new base C (0/15);  total (10/18)
Fisher's exact test for biased strand distribution p-value = 2.18e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.67e-05

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAC  >  NC_000913/357731‑358012                                                                                                                                                       |                                                                                                                                     cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                     <  1:507796/151‑1 (MQ=255)   cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                   >  2:6760/1‑151 (MQ=255)       ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                                                                                                                >  2:187169/1‑150 (MQ=255)         ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                             >  2:506693/1‑151 (MQ=255)         ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaa                                                                                                                             >  1:557133/1‑151 (MQ=255)                 gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                     >  1:507722/1‑151 (MQ=255)                               gCAATTCCAGCCGCGGCCCTGTGTCAGGGGCTCCCGTGATTCATTCCCGCC‑AACAACCGCGAATTTATCCAACGCCATGTGCAAAAAGGCCTTCGCGGCGGCTGTCTCCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                          <  2:456826/148‑1 (MQ=18)                               aaattcccAGCCGCAGCCCTGTGCCAGCGGCTCCCGTGATTCTTTCCCGCC‑AACACCCGCGCTTTTACCCACCCCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCagt                                                                                                       <  1:619248/145‑1 (MQ=255)                                 attcccaccccaggACCTGTGTCAGCGCCTACCGTGATTCATTCCCCCC‑AACACCCGCGCTTTTACCCACCGCCATGTCCAAAAATGCCTCCGCGGCGGCTGTCTGCAAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCagtag                                                                                                     <  1:37431/138‑1 (MQ=255)                                 aaTTCAAGCCGCAGCCCTGTGTCAGCGGCTCCGGTAATTCATTCCCCCC‑AACAACCGGGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGGCTGCCAGCTATTTTCCCGCCGCAACGAAACCGCCGTTCTCTCCagtag                                                                                                     <  1:585061/151‑1 (MQ=18)                                   ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                   >  1:259679/1‑151 (MQ=255)                                    tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACACCCGCGCTTTTATCCAACGCCATGTCAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                  <  2:151626/151‑1 (MQ=21)                                         ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                             >  2:140059/1‑151 (MQ=255)                                                               aCCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGAAAAAACttttatac                                                                        >  2:538824/1‑145 (MQ=25)                                                                      ttCATTCCCCCC‑AACACCCGCGCTTTTACCCACCGCCATGTGAAAAAATGCTTCCGGGGCGGCTGTCGGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgt                                                                <  2:259681/151‑1 (MQ=255)                                                                        cATTCCCCCC‑ACCACCCGCGCATTTCCCCAACCCCATGTGCAAAAAGGCCTCCGGGGGGGCTGTCGGCCAGCTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                              <  1:598417/151‑1 (MQ=255)                                                                        cATTCCCCCC‑AACACCCGCGCATTTATCCACCGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                              <  2:238720/151‑1 (MQ=255)                                                                         ctttCCCCCAAACACCCGCGCATTTACCCACCGCATGGTGCAAAAACGCCTGCGGGGCGGCGGCCGCCCAGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                              <  1:717785/150‑1 (MQ=255)                                                                                cc‑AACACCCCCCCATTCACCCACCGCTATTTCCAAAAAGCCCTCCCCGCCGCCTTTCTCCCAGCTATTTTCCCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                      <  1:408065/151‑1 (MQ=255)                                                                                      acccGCGATTTTACCCAACGCAATGTGAAAAAATCCCTCCGCGGCGCTTGCCGGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                 <  1:342276/149‑1 (MQ=255)                                                                                                 tATCCACCCCCGTGGGAAAAATGGCCTCCGCGGGGGTGGTCTGCCAGCTATTTTTCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                      <  1:377155/151‑1 (MQ=255)                                                                                                  aTCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTTAAACCGTCCTGTTGTGTGGGGAAAGCTGCTggggaaaaa                                     >  2:366481/1‑144 (MQ=25)                                                                                                       ccGCCATGTGAAAAAATCCCTTCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                <  2:480573/150‑1 (MQ=255)                                                                                                          ccATGTGCAAAAAGGCCTCCGCGCCGGCTGCCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                             <  1:291087/151‑1 (MQ=255)                                                                                                              gtgCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTTAAACCCTCATGTTGTGTGGGGATCGCTGCTGGGGACAAAGTGGAAAGGGaa                         >  2:341144/1‑151 (MQ=255)                                                                                                                          ctccggggcggcTGTCTGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc             <  2:492172/145‑1 (MQ=255)                                                                                                                                     cTGTCGGCCAGTTTTTTGCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc  <  1:43454/151‑1 (MQ=255)                                                                                                                                       gTCTGCCAGCTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc             <  2:277864/138‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                     CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAC  >  NC_000913/357731‑358012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑