Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	50.0%	34.6 / 19.3	38	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (17/2);  new base C (0/19);  total (17/21)
Fisher's exact test for biased strand distribution p-value = 1.19e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357739‑358025                                                                                                                                                  |                                                                                                                                                  ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGca                                                                                                                                           >  2:405875/1‑150 (MQ=255) ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGca                                                                                                                                           >  2:450120/1‑150 (MQ=255)     aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACaaa                                                                                                                                      <  2:711974/151‑1 (MQ=255)            tAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTTCC‑AGCTATTTTTCCGCCGCAACAAAAccgccg                                                                                                                               >  1:309877/1‑151 (MQ=255)                gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                           >  2:141516/1‑151 (MQ=255)                 cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                          >  1:377765/1‑151 (MQ=255)                  aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTtctct                                                                                                                         >  2:480804/1‑151 (MQ=255)                    cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                       >  2:92828/1‑151 (MQ=255)                    cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                       >  2:642902/1‑151 (MQ=255)                        cattcccACCCGCAGCCCTTTTTCGCCGGCTCCGGTGATTCTTTCCCGCC‑ACCAC‑CCGCCCTTTTCCCCACCCCCTTGTCCAAAAT‑TGCTTTCGCGGCGCCTTTCTGCC‑CCTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                                     <  2:119585/144‑1 (MQ=255)                          aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                 >  2:55331/1‑151 (MQ=255)                            tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                               >  2:87425/1‑151 (MQ=255)                             ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                              >  1:487165/1‑151 (MQ=255)                                 ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                          >  2:603249/1‑151 (MQ=255)                                  cccAGCCCTGTGTCAGCGCCTCCCGTGATTCATTCCCCCC‑ACCAA‑CCGCGTTTTTACCCACCCCCATGTGAAAAAA‑TCCCTGCGGGGGGGTTGTCGGCC‑ATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGc                                                                                                         <  1:727708/149‑1 (MQ=255)                                  cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                          >  2:38519/1‑150 (MQ=255)                                     aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                         >  1:312360/1‑147 (MQ=255)                                      gccttgtgTCAGCGCCACCCGTGTTTCATTCCCCCA‑AACAC‑CCGCGCTTTTACCCACCGCCTTGTGAAAAAA‑GGCCTTCGGGGCGGTTGTCTCCC‑ATTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                       <  1:396986/145‑1 (MQ=255)                                          tgtggatggggttACTGTGATTAATTCCCG‑C‑AACAACCCGGGCTTTTATCCACCGCCTTGCAAAAAAA‑CGCCTTCGGGGCGCCTTTCTGCC‑AGTTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                       <  2:840692/133‑1 (MQ=255)                                            tgccggCGGCCACCGTTTTTCATTCCCCCC‑ACCAC‑CCGCGCTTTTACCAACCCCCTTTTAAAAAAA‑TCCCTGCGGGGCGGCTGTCTCCC‑AGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                  <  1:244935/143‑1 (MQ=255)                                                aGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGgaaaa                                                                                               >  2:524840/1‑145 (MQ=255)                                                   ggCTCCCGTTATTCTTTCCCCCC‑ACCAC‑CCGCCCTTTTACCCAACCCCATG‑GCAAAAATTGCTTCCGGGGGGGCTGTCTGCA‑GGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                          <  1:597632/149‑1 (MQ=255)                                                    gcctccggtatttctttCCCCCAAACAC‑CCGCCCTTTTACCCACCGCCATGTGAAAAAA‑CGCCTGCGCGGGGGCTGTCTCCC‑AGCTTTTTTCCCGCGAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                                 <  1:55322/128‑1 (MQ=255)                                                        ccGTGTTTCATTCCCCCC‑ACCAC‑CCGCGCTTTTATCCACCCCCATGTGAAAAAA‑TCCCTCCGCGGGGGCTGTCTGCC‑ATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                     <  2:378963/149‑1 (MQ=255)                                                              ttCTTTCCCCCC‑ACCAC‑CCGCGCTTTTACCCACCCCCTTGGGAAAAAA‑TCCCTCCGGGGCGGTTTTCTCCC‑AGTTTTTTTCCCGCCACAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                           <  1:541758/137‑1 (MQ=255)                                                                    tCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTTGCCCGTCAtgt                                                                             >  2:195146/1‑145 (MQ=37)                                                                    cccccc‑AACAC‑CCGCGCTTTTACCCACCCCCATGGAAAAAAA‑TCCCTTCGCGGCGGCTGTCTGCC‑AGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                                        <  2:862511/146‑1 (MQ=255)                                                                           aacac‑cCGCGCTTTTTCCCACCCCAATGTGAAAAAA‑TCCCTCCGCGGCGTCTTTCTCCC‑AGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                  <  2:321177/150‑1 (MQ=255)                                                                                cccGCACATTTACCCACCCCCTTGAAAAAAAA‑CCCTTCCGGGGCGTCTGTCTGCC‑AGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                 <  1:65109/146‑1 (MQ=255)                                                                                 ccGCGCTTTTCCCCACCCCCATGTGAAAAAA‑TGCCTTCGCGGCGGTTGTCTCCC‑AGCTTTTTTCCCGCCGAACAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                    <  1:641477/143‑1 (MQ=255)                                                                                 ccGCGCTTTTACCCACCGCCTTGTGAAAAAT‑TGCCTTCGCGGCGGCTGTCTGCC‑ACTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                               <  2:155336/148‑1 (MQ=255)                                                                                  cgcgCATTTACCCAACCCCATGTAAAAAAA‑TGCCTCCGCGGCGGCTGTCTGCC‑AGTTATTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                           <  2:316885/151‑1 (MQ=255)                                                                                                acgctgtatgtaaaaa‑TACCTACGCGGCGGCT‑AGTGCCTATCTATTTTTCCGCCAAAGGAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                                <  2:745263/137‑1 (MQ=255)                                                                                                        tgCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGAAAAAAATTTAAACCCCCCAAGGTGTGTGGGGATCTCCGCTGGGGACAAAGTGGGAAgg                                         >  2:167454/1‑147 (MQ=255)                                                                                                          aaaaaa‑TGCCTTCGGGGCGGCTGTCTGCC‑AGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                   <  2:893929/150‑1 (MQ=255)                                                                                                           aaaaa‑TGCCCCCGCGGCGGCTTCCTGCC‑AGTTTTTTTCCCGCAGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                    <  1:281193/149‑1 (MQ=255)                                                                                                           aaaaa‑TCCTTCCGGGGCGGTTGTCTGCC‑AGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                     <  2:6437/148‑1 (MQ=255)                                                                                                              aa‑TCCCTTCGGGGGGGCTTTCTCCC‑AGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                               <  2:626853/151‑1 (MQ=255)                                                                                                                                            ttttttcCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc          <  1:105931/142‑1 (MQ=255)                                                                                                                                               ttttCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGGAAAAAAATTTTAAACCCCCATGTTTTGTGGGGAACGCTGCTGGTAACAATTTGGGAAGGGAAGGGGGGGGGATACGCTCCAGAAACGCGCCAATTGAg  >  2:259385/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAA‑TGCCTTCGCGGCGGCTGTCTGCC‑AGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357739‑358025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑