Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	56.1%	19.5 / 47.7	41	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (11/7);  new base C (0/23);  total (11/30)
Fisher's exact test for biased strand distribution p-value = 1.01e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.95e-06

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357730‑358022                                                                                                                                                       |                                                                                                                                                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)                                                                                                                                               gttATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAtt  <  2:969388/149‑1 (MQ=255)                                                                                                                                                 ttttttc‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc         <  1:306391/140‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATT  >  NC_000913/357730‑358022

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: ‑