Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	53.1%	22.2 / 42.8	32	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (12/3);  new base C (0/17);  total (12/20)
Fisher's exact test for biased strand distribution p-value = 2.02e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.33e-06

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357731‑358027                                                                                                                                                             |                                                                                                                                                      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                                                                                                                                         >  2:460330/1‑151 (MQ=255)            gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGcaacaa                                                                                                                                         >  1:223936/1‑151 (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)                                                                                                                                           ttttcggctagtttttttcCC‑G‑CCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                 <  1:892784/137‑1 (MQ=255)                                                                                                                                                          tttcCC‑G‑CCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt  <  1:1161892/151‑1 (MQ=255)                                                                                                                                                             |                                                                                                                                                      CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGT‑CAGCGGCTACCGTGATTCATT‑TCCGCC‑AACAACCGCGCATTTATCC‑AACGCCATGTGCAAAAATG‑CC‑TTC‑GCGGCGGCTGTCTGCCAGCTATTTTTCC‑G‑CCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTT  >  NC_000913/357731‑358027

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: ‑