Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	57.5%	16.8 / 47.8	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (11/6);  new base C (0/23);  total (11/29)
Fisher's exact test for biased strand distribution p-value = 5.35e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.82e-06

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357733‑358019                                                                                                                                                         |                                                                                                                                            cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                          <  2:619690/151‑1 (MQ=255)    aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTccgccg                                                                                                                                       <  2:405187/151‑1 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                  >  2:233563/1‑150 (MQ=255)          gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                   <  1:1114120/149‑1 (MQ=255)           aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                 >  1:24166/1‑150 (MQ=255)                     cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                      >  1:686916/1‑151 (MQ=255)                      gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                     >  2:603625/1‑151 (MQ=255)                        aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CCCCA‑TGTGCAAAAATG‑CTTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                      <  2:663876/148‑1 (MQ=255)                            ggaattcccAGCCGCAGACCTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCC‑AA‑CACCCGCGCATTTACCCAC‑CGCCT‑TGTGAAAAAATC‑CCTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCa                                                                                                                <  2:102271/143‑1 (MQ=255)                             gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                              >  2:1126481/1‑151 (MQ=255)                                 tcccggCCGCGGCCTTGGGTCAGCGCCTCCCGTATTTCATTCCCCCA‑AA‑CACCCGCGCTTTAACCCAA‑CGCCA‑TGTGAAAAAATG‑CCTTCGGGGCGGTTTTTCCCCCGCTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                           <  2:465165/145‑1 (MQ=255)                                   ccggCCGCGGCCCTGTGTCAGCGGCTCCCGTGTTTCTTCCCCCCC‑AA‑CACCCGCGCATTTACCCAC‑CCCCA‑TGTGAAAAAATC‑CTTCCGGGGGGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                         <  2:610951/147‑1 (MQ=255)                                   ccggCCGAAGCCCTGTGTAGGCGGCTCCCGTGATTCTTTCCCGCA‑AA‑CACCCGCGCTTTTACCCAC‑CCCCT‑TGTG‑AAAAATGCCCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                        <  2:587091/148‑1 (MQ=255)                                            gACCTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCC‑AC‑CACCCGCCCATTTACCCAC‑CGCCA‑TGTAAAAAAATC‑CCTTCGGGGCGGCTTTCTGCCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                <  1:68213/150‑1 (MQ=255)                                            gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGACTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                    >  1:890437/1‑146 (MQ=255)                                              cttgtgTCGGCGGCTCCCGTGTTTCATTCCCGCC‑AA‑CACCCGCGCTTTTATCCAC‑CCCCA‑TGTAAAAAAATC‑CTTTCGGGGCGGTTTTCTGCCAGTTTTTTTCCCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                              <  2:965361/148‑1 (MQ=255)                                                 gtgtCAGCGGTTCCCTTTTTTCATTCCCCCC‑AA‑CACCCGCGCTTTTACCCAA‑CCCCA‑TGTGAAAAAATG‑CCTTCGCGGCGGTTGTCTCCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                                             <  2:220684/148‑1 (MQ=255)                                                     cAGCGGCTCCCGTATTTCATTCCCGCC‑AA‑CACCCGCCCATTTACCCAA‑CCCCA‑TGTGCAAAAATC‑CTTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                       <  2:388253/150‑1 (MQ=255)                                                      cggcgccccccttgttCATTTCCCCC‑AACCACCCGCGCTTTTACCAAC‑CCCCA‑TGTAAAAAAATC‑CCTCCGCGGCGCTTGTCGGCCAGTTTTTTTCCCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGc                                                                                       <  1:1009433/136‑1 (MQ=255)                                                      aGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggcgggaaaaaaaat                                                                                     >  2:768916/1‑136 (MQ=255)                                                         ggCTCCCGTG‑TTCCTTTCCCCCAAA‑CACCCGCG‑ATTTTCCCAACCCCCT‑TGTAAAAAAATG‑CTTTCGGGGGGGCTGTCGCCAAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                                                      <  1:961044/147‑1 (MQ=255)                                                         gcctcccGTTATTCATTCCCCCC‑AA‑CACCCCCGCTTTTACCCAC‑CCCCA‑TGTGAAAAAATG‑CTTTCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                  <  1:962104/146‑1 (MQ=255)                                                           cTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTT‑GCGGCGGCTGGCTGCCAGCTATTTTTCCGCCGCAACAAAAACGCCGGTCTCTCCAGTAGTGGCgggggcaggggaaaaa                                                                                        >  1:894068/1‑130 (MQ=21)                                                              ccGTGATTCTTTTCCCCA‑AA‑CACCCGCGCATTTACCCAA‑CGCAT‑TGTGAAAAAATG‑CCTTCGCGGCGGTTTTCTGCCAGCTTTTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                               <  2:533608/149‑1 (MQ=255)                                                                gTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAACAGGAAAAACttttaaa                                                                                >  2:604540/1‑142 (MQ=25)                                                                      cATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGCGAAAAAGAttttaaacc                                                                              >  1:384259/1‑136 (MQ=255)                                                                      cATTCCCCCA‑AA‑CACCCGCCCTTTTA‑CCAA‑CCCCATTGTAAAAAATTG‑CCTCCGCGGCGGTTGTCTGCCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgtt                                                                      <  2:573978/150‑1 (MQ=255)                                                                        tttCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAACttttaaaccctcctgtt                                                                      >  2:478419/1‑134 (MQ=25)                                                                                  accacccGCTCTTTTATCCAC‑CGCCA‑TTTGAAAAAAGC‑CTTTGGCGGGGGCTTTCTCCCAGTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                           <  2:171444/146‑1 (MQ=255)                                                                                       cgccgcTTTTACCCAC‑CGCCT‑TGTGCAAAAATG‑CCTTCGCGCCGCTTGCCTGCCAGTTTTTTTCCCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                        <  1:550279/146‑1 (MQ=255)                                                                                               ttACCCAC‑CCCCA‑TGGGAAAAAATG‑CCTCCGGGGGGGCTGTCTCCCATTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                               <  1:1126341/150‑1 (MQ=255)                                                                                                        ccccA‑TGTGAAAAAATG‑CCTCCGGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                       <  2:97579/148‑1 (MQ=255)                                                                                                        cGCCA‑TGTGCAAAAACG‑CTGTCGCGGCGGCTGTCTGCCACCTTTTTTCCCGCCCCACAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                        <  2:1104703/149‑1 (MQ=255)                                                                                                                   aaaaaGG‑CCTTGGCGGGGGTTGTCTGCCACTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                              <  1:975486/149‑1 (MQ=255)                                                                                                                                     gtcttcctccaggttATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg            <  1:489350/136‑1 (MQ=255)                                                                                                                                     gctggccgcccAGTTTTTTTCCCGCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTcc              <  1:763769/139‑1 (MQ=255)                                                                                                                                      gcTGTCTGCAAGTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa           <  1:108049/150‑1 (MQ=255)                                                                                                                                       cTGTCCGCCATTTTTTTTCCCCCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa           <  2:55430/149‑1 (MQ=255)                                                                                                                                              ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  2:564846/151‑1 (MQ=255)                                                                                                                                              ccAGTTATTTTTCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa  <  1:77025/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                            CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357733‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑