Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.3%	6.4 / 40.4	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (9/9);  new base A (0/19);  total (9/28)
Fisher's exact test for biased strand distribution p-value = 3.91e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.47e-02

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAT  >  NC_000913/357742‑358036                                                                                                                                                          |                                                                                                                                                   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)                                                                                                                                              ttcccgccgCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt           <  2:1114754/147‑1 (MQ=255)                                                                                                                                                 ccgccgAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc          <  1:68363/148‑1 (MQ=255)                                                                                                                                                        aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAt  <  2:79437/149‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                                   GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAAT  >  NC_000913/357742‑358036

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: ‑