Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,873	0	C	T	46.7%	11.5 / 18.9	34	S273N (AGC→AAC)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (12/4);  new base T (1/13);  total (14/20)
Fisher's exact test for biased strand distribution p-value = 2.30e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGC  >  NC_000913/357728‑357993                                                                                                                                                         |                                                                                                                           gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTAttt                                                                                                                       >  2:65503/1‑151 (MQ=255)    cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGGTGCCTGCCAGATAttttta                                                                                                                    >  1:1706/1‑150 (MQ=255)      cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTcc‑g                                                                                                                 >  1:726052/1‑151 (MQ=255)      cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTcc                                                                                                                   >  1:294329/1‑150 (MQ=255)        tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTcc‑g‑c                                                                                                               <  2:842939/150‑1 (MQ=255)            ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGcaa                                                                                                          >  1:1007638/1‑151 (MQ=255)            ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGcaa                                                                                                          >  1:274986/1‑151 (MQ=255)            ccTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGCGT‑CAGCGGCTACCGTGATTAATT‑TCCGCC‑AACAACCCCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGCTTGTCTGGCAGTTATTTTTCc‑c‑ccgcca                                                                                                          >  1:475412/1‑149 (MQ=17)               gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGcaacaa                                                                                                       >  1:223936/1‑151 (MQ=255)               gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGcaacaa                                                                                                       >  2:460330/1‑151 (MQ=255)                    gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAAccg                                                                                                  >  1:89092/1‑151 (MQ=255)                                aGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCa                                                                                      >  2:995189/1‑151 (MQ=255)                                    tgtcccAGCAGCGGACGTGTGC‑CGGCGGCTCCGGTGTGTCATC‑CCCGCC‑ACCACGCGCGCATTCCCCC‑AGCGCTAGGTG‑AAAAACG‑CC‑TTCGGCGGGGGTTGTCCGCCAGTTTTTTTCCG‑G‑CCGAAAAAAAACCGCCGTTCTCTCCagtag                                                                                  <  2:184611/147‑1 (MQ=255)                                    attccccgCCGAAGCCCTGTGT‑CAGCGGCTACGGTGTTTCTTT‑CCCCCC‑AACAACCGCCCTTTTTCCC‑ACCGCCTGGTAAAAAAAGG‑CT‑TCC‑GCGGCGGTTTTCTCCCGGTTTTTTTCCC‑G‑CCGAAAAAAAACCGCCGTTCTCTCCagtag                                                                                  <  1:1216912/144‑1 (MQ=255)                                    atccccgcccGCAG‑CCTTTGTCCAGCGCCTCCCGTG‑TTCATTCCCCGCC‑AACAACCGCGCTTTTCCCC‑CGC‑CCATTGGAAAAAATT‑CCTTTC‑GCGGCGTCTTTCTGCCTTTTTTTTTCCC‑C‑CCCCAACAAAACCGCCGTTCTCTCCagtag                                                                                  <  2:668385/143‑1 (MQ=255)                                         cccccGCAGCCCTTTGT‑CGGCGCCTCCCGTTTTTCTTT‑CCCGCC‑ACCACCCGCGTTTTTCCCC‑ACCCCAATGTCAAAAAATG‑CC‑TCC‑GGGGCGGTTTTCGGCCAGTTTTTTTCCC‑G‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                             <  1:262390/148‑1 (MQ=255)                                                 gatcTGTGT‑CAGCGGCTACCGTGATTCATT‑CCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGCTCTCTCCAGTAGTGGCggggtctgg                                                                     >  2:687475/4‑146 (MQ=255)                                                   cgtgtgT‑CAGCGCCTACTGT‑TTTCCTT‑TCCCCCAAACACCCGCG‑ATTTACCCAAACGCCATG‑GAAAAAACGCCC‑TCC‑GCGGGGGTTGCCGCCCATTTTTTTTCCC‑G‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgaga                                                                   <  2:1100560/149‑1 (MQ=255)                                                   ccTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggaggga                                                                   >  2:652098/1‑144 (MQ=255)                                                           tacgcgttacctgtatttatt‑tCCGCC‑AAACACCGCCTATTTAACC‑AACGCCATGGGAAAAAAGT‑GC‑TTC‑GGGGGGGCTTGCTGGCGGGTAGTTTTCCGG‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCACGAGAAATAg                                                              <  2:685683/136‑1 (MQ=255)                                                             tcGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGagctgcaaagcaat                                                          >  2:1089367/2‑139 (MQ=255)                                                              cggcaccggTGATTCTTT‑CCCCCC‑ACCACCCCCGTTTTAATCA‑ACCGCCTGGCGAAAAAATC‑CT‑TCC‑GCGGGGGTTGTCGGCC‑GGTTTTTTTCC‑GCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCt                                                            <  2:796699/140‑1 (MQ=255)                                                                  tgcgagtttccATT‑CCCCCC‑AACACCCGCGCTTTAACCC‑ACCTCAATGTGAAAAAATG‑CT‑TCC‑GAGGTGGGTTGCGGCCACTTTTTTTCCC‑G‑CCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                     <  2:98527/141‑1 (MQ=255)                                                                  tacgggtttccATT‑CCCCCC‑AACACCCGCGCTTTACCCC‑ACCGCAATGAGAAAAAATG‑CC‑TCC‑GCGGGGGTTGCCGCCGAGTTTTTTTCCC‑G‑CAACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                     <  2:655922/141‑1 (MQ=255)                                                                            cATT‑CCCCCC‑AACACCCGCGTATTTACCC‑ACCGCAATGTAAAAAAAGC‑CC‑TTC‑GGGGCGGCTGTCGGCCAGTTTTTTTCCC‑G‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                           <  1:460479/151‑1 (MQ=255)                                                                            cATT‑CCCCCA‑AACACCCGCGATTTTACCC‑ACCGCCTTGAGAAAAAATG‑CC‑TGG‑GGGGGGGTTGTCTGCCAGTTTTTTTCCC‑G‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                           <  2:318482/151‑1 (MQ=255)                                                                             ttttcccccc‑AACAACGCCACATTAACCA‑AACGCCTTGTAAAAAATTG‑CC‑GTC‑GCGGCGGTTGTCGCCCTGCT‑TTTTCCC‑GCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                           <  2:1094009/143‑1 (MQ=255)                                                                             ctttcccccc‑AACACCCGCCCTTTTACCA‑ACCCCCATGTCAAAAAATC‑CC‑TTC‑GCGGGGGCTGTCGGCCAGTTTTTTTCCC‑G‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                           <  1:198173/143‑1 (MQ=255)                                                                              cttccccccaaacaccCGCTCTTTTACCC‑ACCCCCATGTCAAAAAATG‑CT‑TGG‑GGGGCGGCTGTTGGCCAGTTTTTTTCCC‑G‑CCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttg                                           <  1:993927/141‑1 (MQ=255)                                                                                                    tttACCC‑ACCCCCATGTGAAAAAATC‑CC‑TCC‑GGGGCGGCTGTCTGCCAGCTTTTTTCCC‑C‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                     <  1:568544/151‑1 (MQ=255)                                                                                                    tttACCC‑ACCCCAATGTAAAAAAATC‑CC‑TCC‑GCGGGGTCTGTCGCCCAGTTTTTTTCCC‑G‑CCGAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                     <  1:206740/151‑1 (MQ=255)                                                                                                    ttcaccc‑ACCGCCGTGTACAAAAATC‑CC‑TCC‑GCGGCGGCTGTCTGCCGGGTATTTTCCC‑G‑CCCCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                     <  2:947730/146‑1 (MQ=255)                                                                                                                      gCAAAAAGC‑CC‑TGC‑GCGGGGCTTGTCGGCAACCTTTTTTCCC‑C‑CCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg     <  2:398518/150‑1 (MQ=255)                                                                                                                        aaaatTG‑CC‑TTC‑GCGGCGGTTGTCTGCCAGTTTTTTCCCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc  <  2:927648/151‑1 (MQ=255)                                                                                                                                                         |                                                                                                                           GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGC  >  NC_000913/357728‑357993

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑