Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	56.0%	7.8 / 30.6	26	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (7/4);  new base T (0/14);  total (8/18)
Fisher's exact test for biased strand distribution p-value = 6.86e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.22e-04

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAC  >  NC_000913/357728‑358012                                                                                                                                                    |                                                                                                                                          gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTag                                                                                                                                          <  1:259918/149‑2 (MQ=255) gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                        >  2:816345/1‑151 (MQ=255)      cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                   >  2:382174/1‑151 (MQ=255)      cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                                    >  2:345581/1‑150 (MQ=255)           gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCcgccgc                                                                                                                               >  2:383954/1‑150 (MQ=255)                   aGCGTAGCGCATCAGGAAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                      <  1:581863/151‑1 (MQ=255)                         gcgcATCAGGCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTCCTCCAACGCCATGTGCAAAAATGCCTTCGCAGCGGCCGTCTGCCAGCTGTCTTTtcgccccgatacggcggcc                                                                                                                   >  1:779590/1‑134 (MQ=14)                                     aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagtagt                                                                                                    >  2:527925/1‑151 (MQ=255)                                                          cAGCGCCTCCCGTGATTCTTTCCCCCAAACACCCCCTCTTTTCCCCACCCCCATGGGAAAAAATCCCTCCGCGGCGGCTGTCTGCAGGCTATTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                  <  1:243381/148‑1 (MQ=255)                                                                 tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAgacataatc                                                                         >  1:864329/1‑142 (MQ=25)                                                                             ttccccccAACACCCGCGCTTTTCCCAAACCCCTTTTGAAAAAATGCTTCCGGGGCGGCTGTCTGCCAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                             <  2:633630/144‑1 (MQ=255)                                                                              ttCCGCCAACACCCGCGCATTTACCCACCCCCATGTGCAAAAATGCCTTCGCGGCGTTTGTCTCCCAGCTTTTTTTCCGCCTCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                                              <  2:127329/148‑1 (MQ=38)                                                                               ccccccAACACCCGCGCTTTTACCCAACCCTGTGTAAAAAAATGCCTCGGCGGGGGCTGCCGCCCAGCTTTTTCCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgtg                                                          <  1:275568/147‑1 (MQ=255)                                                                                ccccaaacaccCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTTCGGGGGGGCTGTCTGCCAGTTATTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg                                                            <  2:578753/143‑1 (MQ=255)                                                                                ccGCCAACACCCGCGTTTTTACCCACCGCCTTGTGAAAAAATGCCTTGGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                         <  2:645705/151‑1 (MQ=255)                                                                                             ctcttttACCCACCCCCTTGTAAAAAATTCCCTTCGGGGCGGCTTTCTGCCATTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                              <  2:713622/145‑1 (MQ=255)                                                                                                  ttATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACTTTAAACCCCTCCCGTtgtttg                                                          >  2:31119/1‑132 (MQ=37)                                                                                                      ccAACGCCATGTGAAAAAATGCTTCGGGGGGGGCTTTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                     <  2:293288/149‑1 (MQ=255)                                                                                                        acccccttgtgAAAAAATCCCTTCGGGCGGGTTTTCGCCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                      <  2:848012/139‑1 (MQ=255)                                                                                                        acccccATGTGAAAAAATCCTTCCGCGGGGGCTGTCTCCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                  <  2:735715/146‑1 (MQ=255)                                                                                                        aaCCCCATGTCAAAAAAGGCCTTCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                       <  2:153508/145‑1 (MQ=255)                                                                                                          ccccttgtgAAAAAAGCCCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                <  2:507651/145‑1 (MQ=255)                                                                                                                    agaaaTGCCGTCGCGGCGCCTGTTTCCAAATTATTTTTCCCGCTAAACAAACCCGTCGTTCTCTCCAGTAGTGGCTGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                      <  2:511426/148‑1 (MQ=255)                                                                                                                    aaaacTGCCTCCGCGGCGGCTGTCTGCAACCTTTTTTCCCGCCCAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                        <  2:449313/148‑1 (MQ=255)                                                                                                                                  ggcggcTGTCTGCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa            <  1:81180/146‑1 (MQ=255)                                                                                                                                           cTGCCATTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc  <  2:488614/147‑1 (MQ=255)                                                                                                                                              ccAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa      <  1:605790/140‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                          GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAC  >  NC_000913/357728‑358012

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: ‑