Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	44.4%	61.1 / 20.9	46	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (22/3);  new base A (0/20);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 6.32e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357741‑358033                                                                                                                                                        |                                                                                                                                                    tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aac                                                                                                                                                     >  1:856884/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aaca                                                                                                                                                    <  1:782040/150‑1 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAcc                                                                                                                                               <  1:698788/151‑1 (MQ=255)         gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAAccgcc                                                                                                                                            >  2:462865/1‑151 (MQ=255)            gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGtt                                                                                                                                         >  1:1048756/1‑151 (MQ=255)             cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGtt                                                                                                                                         >  1:611138/1‑150 (MQ=255)                aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTtctct                                                                                                                                     >  1:904942/1‑151 (MQ=255)                       attcccggCCGCAGCCTTGTGCCAGCGTCTCCCGTAATTCATTCCCCCAAACACCCGCGCATTTACCCACCGCCATGTGAAAAAATCCC‑TCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCagta                                                                                                                               <  1:766295/143‑1 (MQ=255)                         ttCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                            >  2:152116/1‑151 (MQ=255)                           ccccccgaagtcttgtgTCACCGCCCGCGGTAATTTATTCCCGCCAACACCCGCCCTTTAACCCAACCCATTGTCAAAAAAGGCC‑TTGGCGGCGGCTTTCTGCCATTTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                            <  1:416897/136‑1 (MQ=255)                           ccccccGCAGCCTGGTTTCGGCGGCTCCCGTGTTTCTTTCCCCCCACCACCCGCGCTTTTATCCAACCCCATGTAAAAAAAGGCC‑TCCGGGGCGGCTGTCGGCAAGTTTTTTTCCCGCCGA‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGc                                                                                                                          <  2:108709/147‑1 (MQ=255)                           ccAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                          >  1:123461/1‑151 (MQ=255)                            cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                         >  2:528241/1‑151 (MQ=255)                            cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                         >  2:153861/1‑151 (MQ=255)                             aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  1:494239/1‑151 (MQ=255)                               ccgcattcttgtgTCGGGGGCTCCCGTGATTCATTCCCCCCAACACCCGCCCTTTTCCCAACCGCATTGTCAAAAAATGCC‑TTCGCGGCGGCTGTCTCCCGGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       <  1:320622/141‑1 (MQ=255)                               ccccacccttttctCAGCGCCTCCCGTTTTTCTTTCCCCCCAACACCCGCCCTTTCACCCACCGCATTATCCAAAAATCCC‑TTCGCGGCGCCTTCCTGCATGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                            <  2:115105/132‑1 (MQ=255)                                cGCAGCCTTGTGCCGGCGCCTCCCGTTTTTCTTTCCCCCCAACACCCGCCTTTTTCCCAAACCCCTTGTAAAAAAATCCC‑TCGGCGGCGGCTGTCTGCC‑GTTTTTTTTCCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        <  2:584488/148‑1 (MQ=255)                                cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCGGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        >  2:1061829/1‑148 (MQ=255)                                cGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                     >  2:419476/1‑150 (MQ=255)                                 gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggg                                                                                                                    >  1:247192/1‑149 (MQ=255)                                      ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       >  1:644083/1‑143 (MQ=255)                                               gCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGG‑aaaaaagatt                                                                                                     >  2:566249/1‑144 (MQ=255)                                               gCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑CTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggggaggaaaaaaat                                                                                                       >  2:421871/1‑135 (MQ=25)                                                 ggCTCCCGTTTTTCTTTCCCCCAAACACCCCCCCTTTTACCAACCGCCAGGTGAAAAAATGCC‑TGCGGGGGGGCTGTCTCCCAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑ttt                                                                                                    <  2:882142/149‑1 (MQ=255)                                                 ggCTACCTTGTTTCTTTCCCCCCAACACCCGCCCATTTACCCAACCCCATGTGAAAAAATGCC‑TCCGCGGGGGCTTTCTGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATa                                                                                                          <  1:705072/144‑1 (MQ=255)                                                 gcctcccttatttCTTTCCCCCCACCACCCGCGTTTTTACCCAACCCCATGT‑CAAAAAAGCCTTTCGCGGGGGTTTTCTGCAAGCTTTTTCCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑tt                                                                                                     <  2:247208/137‑1 (MQ=255)                                                     aCCGTGATTCATTTCTGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑aaaaaaaatttaacac                                                                                               >  1:139267/1‑138 (MQ=25)                                                     aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGAG‑aaaaaaatttttga                                                                                                 >  1:642313/1‑138 (MQ=25)                                                      ccgtttttCTTTCCCCCCAACACCCGCGCTTTTACCCACCGCCTTGTGAAAAAATGCT‑TCCGGGGGGGCTGTCGGCCAGTTTTTTTCCCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGcc                                                                                               <  1:478985/143‑1 (MQ=255)                                                      ccGTGATTCATTCCCCCAACCACCCCCGCTTTTACCCACCGCCATGTGAAAAAATCCT‑TCCGGGGCGGTTTTCTCCAAGTTTTTTTCCCCCCAA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGcc                                                                                               <  1:1038811/149‑1 (MQ=255)                                                                ttccccccaccaCCCGCGTTTTTCTCCACCGCCAGGTAAAAAACTGCC‑TCCGCGGCGTTTGTCTCCCATTTATTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCAtgttgt                                                                                    <  2:440534/144‑1 (MQ=255)                                                                ttccccccAACACCCGCGCTTTTACCAAACCCCTTGTAAAAAAATCCC‑TCCGGGGGGCCTGTCTGCCAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCAtgttgt                                                                                    <  2:471431/144‑1 (MQ=255)                                                                   ccccaaacaccCGCGCTTTTACCCACCGCCATGTGAAAAAATGCC‑TCCGGGGCGGCTTTCTGCAAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCAtgtt                                                                                      <  1:754801/140‑1 (MQ=255)                                                                             ccGCGCTTTTACCCACCGCCTTGTGAAAAATTGCC‑TTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCgc‑t                                                                       <  1:349663/149‑1 (MQ=255)                                                                                     ttATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGTGAGAGAAAAAAGC‑TTTAACCCCCTCacttgggt                                                                                   >  2:533874/1‑124 (MQ=25)                                                                                                          aacgCC‑TCCGGGGGGCCTTTCTGCCATTTTTTTTCCCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTgcggc                                       <  2:790852/148‑1 (MQ=255)                                                                                                                    gcggcgGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAGT‑TTTAAACCCCCCTTGTT‑TGTGGGGATCGC‑TCCTGGGGAAAAAGTGGGAAAGGGaggggggggg                                      >  1:546323/1‑135 (MQ=255)                                                                                                                      ggcggcTTTCCGCAAGCTTTTTTCCCGCCGA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGc                               <  1:1096753/148‑1 (MQ=255)                                                                                                                       gggcgtttcggcaaGCTTTTTTTCCTCCGA‑AATAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCa                           <  1:842949/138‑1 (MQ=255)                                                                                                                        cggcTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCCGAG‑AAAAAAC‑TTTTAAACCCCCATGGTTTGTGGGCATGGC‑CGCTTGGTACAAATT‑GGGAAGGGGAGGgcgggggaaaacctccc                           >  2:220295/1‑137 (MQ=255)                                                                                                                         ggcTGTCGCCCCGTTTTTTTCCCCCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAg                          <  2:528755/150‑1 (MQ=255)                                                                                                                               caccttttttttttcCCGCCGC‑AAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTcc                            <  2:494241/132‑1 (MQ=255)                                                                                                                                tGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGTGAACAG‑AAAAAACTTTTAAACCCG‑CTTATTGTGTGGGGATCGCTTGCCGGGAA‑AAAAA‑GGAAAGGGAAAGGCGGGGGATCCGCGCCAGaa                        >  1:29988/1‑145 (MQ=255)                                                                                                                                  ccAGTTTTTTTCCCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                  <  1:566230/149‑1 (MQ=255)                                                                                                                                         ttttcCCCCCCC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa           <  2:278981/149‑1 (MQ=255)                                                                                                                                              ccgccgA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGcc    <  1:1030171/151‑1 (MQ=255)                                                                                                                                                cgccaaaacaaATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc       <  1:646735/141‑1 (MQ=255)                                                                                                                                                  cgc‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAG‑AAAAAAC‑TTTTAATCCCCCCCGTTTTGTGGGCATTGC‑TGCTGGGGACAAAGT‑GGGAAAGGGAGAGCGGGGGAACAACTCCCGAACCGCCCCAATTTAGTTTGcccc  >  1:529215/1‑147 (MQ=255)                                                                                                                                                        |                                                                                                                                                    TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGC‑TGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTC  >  NC_000913/357741‑358033

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: ‑