Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	41.5%	28.6 / 19.6	42	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/11);  new base T (0/17);  total (13/29)
Fisher's exact test for biased strand distribution p-value = 1.50e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAA  >  NC_000913/357723‑358020                                                                                                                                                       |                                                                                                                                                     gCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGc                                                                                                                                                      >  1:295429/1‑151 (MQ=255)   aCTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCt                                                                                                                                                     >  2:9475/1‑150 (MQ=255)        aCTCGTAGTCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGAGATTCATTTCCGCCAACAACCGCGCATTTATCCTACGCCATGTGCAAAAATGCCTTCTCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                               >  1:316978/1‑151 (MQ=255)           cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccg                                                                                                                                           >  2:37097/1‑151 (MQ=255)             tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgc                                                                                                                                          <  2:306507/150‑1 (MQ=255)              aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑ccgcc                                                                                                                                         >  1:422947/1‑150 (MQ=255)               ggCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑Ccgccgc                                                                                                                                       >  2:473462/1‑151 (MQ=255)                gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGca                                                                                                                                      <  2:83423/151‑1 (MQ=255)                   tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                    >  2:531894/1‑150 (MQ=255)                      tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                                 >  1:660100/1‑150 (MQ=255)                         gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                             <  1:860580/151‑1 (MQ=255)                          cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                            >  1:389379/1‑151 (MQ=255)                                            tccctccgccgCCCTGTGTCCGCGGCTACCGTGATTCATTTCCGCCAACACCCGCGCATTTCTCCAACGCCCTGTGCCCAACTGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACACAACCGCCGGTCTCTCCAGTAGTgg                                                                                                          >  2:825005/6‑151 (MQ=255)                                            tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                          >  2:936863/1‑151 (MQ=255)                                              cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                        >  1:550081/1‑151 (MQ=255)                                                  cGCAGCCTTGTGTCGGCGGCTACGGTGATTCATTCCCCCCAACCCCCGCGCATTTATCCAACCCCTTGTAAAAAAATGCCTTCGCGGCGGCTGTGTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                     <  1:321771/150‑1 (MQ=255)                                                     agcccTGTGCCAGCGCCTCCGGTTTTTCATTCCCCCCAACACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATGCTTTCGGGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                   <  1:930493/146‑1 (MQ=255)                                                        ctggtgcCAGGGTCTACCGTGTTTCTTTCCCCCAAACACCCGCCCATTTACCCAACGCCTTGTGAAAAAATCCCTTCGGGGCGGCTGTCGCCCAGCTTTTTTT‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                <  2:828862/146‑1 (MQ=255)                                                                  cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGCGGGAGaaaaaaacttt                                                                                    >  1:436179/1‑143 (MQ=25)                                                                  cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCCATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGccaagaaaaggac                                                                                        >  2:251556/1‑135 (MQ=255)                                                                        ccgtttttCTTTCCCCCCAACAACCGCGCATTTCTCCACCCCTGTGTCAAAAAATGCCTTCGCGGCGGCTGTCCCCCAGTTTTTTTT‑CCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                                  <  2:852710/141‑1 (MQ=255)                                                                        ccGTGTTTCATTCCCCCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                   <  2:394079/146‑1 (MQ=25)                                                                        ccGTGATTCTTTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGGGAAAAAATGCCTTCGGGGCGGCTGTCTCCCAGCTATTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                <  2:87903/149‑1 (MQ=255)                                                                              ttCTTTCCCGCCAACACCCGCGATTTTACCCACCGCCATGTAAAAAAATGCCTTCGCGGGGGCTGTCTGCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                           <  2:1045043/148‑1 (MQ=255)                                                                                   tcccGCCACCACCCGCCCATTTACCCACCCCCTTGGAAAAAAATCCCTCCGGGGGGGTTGCCTGCCGGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                     <  1:673021/147‑1 (MQ=255)                                                                                    ccccccAACCCCCGCGCATTTACCCACCGCATTGGAAAAAAGTGCCTCCGGGGGGGTTGCCTGCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                          <  1:432774/139‑1 (MQ=255)                                                                                     cccccAACACCCGCGCTTTTCCCCACCGCCTTGTGAAAAAATCCCTCCGCGGCGGTTTTCGCCCAGTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTc                                                                            <  1:942141/137‑1 (MQ=255)                                                                                               ccGCGTTTTTACCCACCCCCATGTGAAAAAATGCCTTCGCGGCGTCTGTCTCCCAGCTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                       <  1:118528/151‑1 (MQ=255)                                                                                                 gcgcTTTTCCCCACCGCCATGTGAAAAAATCCTTGCGCGGCGTCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                      <  1:878699/150‑1 (MQ=255)                                                                                                 gcccttttCTCCACCGCCAGTTGAAAAAAGCCCTCCGCGCCGGCTTTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                         <  1:639690/142‑1 (MQ=255)                                                                                                             aaCGCCATGTGAAAAATTGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                          <  2:304770/150‑1 (MQ=255)                                                                                                              accctaTGTACAAAAAGGCCTCCGCGGCGGCTTTCTGCCATCTATTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                        <  1:570065/146‑1 (MQ=255)                                                                                                                 catttggaaaaaaTGCCTGCGGGGGGGCTGTCCGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgtg                                          <  1:903764/138‑1 (MQ=255)                                                                                                                         aaaaaTGCCTCGCCGGGGGCTTTCT‑CCAGGTTTTTTTCCCCCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                                    <  1:599695/144‑1 (MQ=255)                                                                                                                         aaaaaGCCCTCCGCGGCGGCTTTCGCCCGGTTTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                             <  2:715029/151‑1 (MQ=255)                                                                                                                          aaagtcccTCCGGGGGGGCGGTCTCCCTGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                            <  1:764350/145‑1 (MQ=255)                                                                                                                             agccttccggggcggtTCTCTCCCTGTTTTTTTC‑CCCCCGAAACAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcggc                          <  1:466095/140‑1 (MQ=255)                                                                                                                                 ctccggggcggcTTTCTGCCAGTTTTTTTC‑CCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                        <  1:618512/142‑1 (MQ=255)                                                                                                                                     ggggcggcTGTCTGCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                    <  2:295477/146‑1 (MQ=255)                                                                                                                                           gcTGTCTGCAGGTTTTTTTC‑CCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa              <  1:542714/148‑1 (MQ=255)                                                                                                                                              gTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc         <  1:945116/150‑1 (MQ=255)                                                                                                                                                cTGCCTCCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg        <  1:192729/149‑1 (MQ=255)                                                                                                                                                     aGCTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTaa  <  2:113316/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     GCACTGAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAA  >  NC_000913/357723‑358020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑