Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	48.8%	35.7 / 21.2	43	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (12/10);  new base T (0/21);  total (12/31)
Fisher's exact test for biased strand distribution p-value = 6.13e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357728‑358019                                                                                                                                                         |                                                                                                                                                 gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                               <  1:173415/151‑1 (MQ=255) gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTAttt                                                                                                                                               <  2:242655/151‑1 (MQ=255)  aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTAtttt                                                                                                                                              >  2:914507/1‑151 (MQ=255)      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)                                                                                                                                                         |                                                                                                                                                 GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTA  >  NC_000913/357728‑358019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑