Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	2,856,886	0	T	G	43.3%	0.6 / 10.7	30	S297A (TCG→GCG)	hdfR_4	HTH‑type transcriptional regulator HdfR
Reads supporting (aligned to +/- strand):  ref base T (1/16);  new base G (5/8);  total (6/24)
Fisher's exact test for biased strand distribution p-value = 6.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GCCAGCGACCTGGTGGGCGAGCCGCTCATCAACGAGGAAATGGTGGTGCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACTGGTGCGTTCGGACATGCTGGCGGCGGTGTCT  >  KT2440/2856751‑2857020                                                                                                                                        |                                                                                                                                       gCCAGCGACCTGGGGGGCGAGCCGCTCATCAACGAGGAAATGGTGGTGCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGGGCTGGGTGTTGCCGCGGGCCGGCTc                                                                                                                                       <  8:378052/137‑1 (MQ=255) cccAGCGACCTGGTGGGCGAGCCGCTCATCAACGAGGAAATGGGGGTGCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCTc                                                                                                                                       <  5:154999/136‑1 (MQ=255)    aGCGACCTGGTGGGCGAGCCGCTCATCAACGAGGAAATGGTGGTGCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCGCGcc                                                                                                                                    >  4:227522/1‑137 (MQ=255)        aCCTGGTGGGCGAGCCGCTCATCAACGAGGAAATGGTGGTGCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGGCGGGGggccggcc                                                                                                                                >  7:411314/1‑137 (MQ=255)              ggggCGAGCCGCTCATCACCGAGGAAATGGTGGGGCGGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAg                                                                                                                          <  7:303500/136‑1 (MQ=255)              ggggCGAGCCGCTCATCAACGAGGAAATGGTGGTGCTGGCCCGTGGGGGGCACCGGCTGTTGCACACTCCCCTGACGCTCACGGGCGTGCACCAGGCGCGCGGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAg                                                                                                                          <  4:185769/136‑1 (MQ=255)                                        aTGGGGGGGCTGGCCCGTCGGGGGCACCCGCGGTGGCACACTCACCTGACGCTCACGGGCGTGCACCTGCCGCGCTGGGGGTTGCCGCGGGCCGGCTCGCCGGCCGGTCAGCTGCTCGACAACTGCTTcgccgccgc                                                                                                <  6:182961/137‑1 (MQ=255)                                          gggggggCTGGCGGGGCGGGGCCACCCGCTGTTGCACACGCACCGCAGGCTCAAGGGCGTGCACCCGGCGCGGGGGGGGTGGCCGCGGGCCGGGGCGCGGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCgg                                                                                              <  8:182507/131‑1 (MQ=255)                                             ggggCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCCCCTGACGCTCAAGGGCGTGCACCCGGCGCGGTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGcc                                                                                           <  1:361528/134‑1 (MQ=255)                                                    gCCCGGCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCGGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAgc                                                                                    <  8:157224/137‑1 (MQ=255)                                                       cGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCGCGCCGGCCCGGCAGCTGCGCGACCACTGCTTCGCCGCCGCGGGCCGGCCCGCGcc                                                                                 >  7:302441/1‑137 (MQ=255)                                                         gggggggCACCCGCGGTGCCACCCTCCCCTCCCGCTCACGGGCGGGCACCAGGCGCGCGGGGGGTTGCCGCGGGCCGGCGCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGt                                                                               <  3:363854/135‑1 (MQ=255)                                                           gggggCACCCGCGGTGGCCCACTCACCTGCCGCTCACGGGCGTGCACCAGGCGCGCTGGGGGTGGCCGCGGGCGGGCTCGCCGGCCGGTCAGCTGCTCTACAACTGATTCGCCGCCGCGGGCCTGACAGCGCCGTgg                                                                             <  8:143124/137‑1 (MQ=255)                                                                   ccGCGGTTGCACACTCCCCTGACGCTCACGGGCGTCCACCTGGCGCGCGGGGTGTTGCCGCGGCCCGGCGGGCGGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCggtggt                                                                     <  7:63277/137‑1 (MQ=255)                                                                      cTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGGCGGCGCGCCGGGCCGGCCGCGGGGCGCCCACGGCGTGCCCGCCGCGGGCCGGGCCGCGCCGGGGGCggggggggg                                                                  >  7:124395/1‑136 (MQ=255)                                                                         ttGCAAACTCACCTGACGCTCAAGGGCGTGCACCAGGCGGGCTGGGTGTTGCCGGGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAg                                                               <  1:25239/137‑1 (MQ=255)                                                                          tGCCCACGCACCTTCCGCTCACGGGCGGGCACCAGGCGCGGTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAgc                                                              <  8:66087/137‑1 (MQ=255)                                                                                     ctcaCGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGc                                                   <  4:369925/134‑1 (MQ=255)                                                                                     cTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGc                                                   <  6:425231/137‑1 (MQ=255)                                                                                         cgcgCACGGGCGGCCACCAGGCGGGGGGGGTGTTGCGGGGGGCCGGCGCGCCGCCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGtt                                               <  3:286141/137‑1 (MQ=255)                                                                                             ttaGGGCGTGCACCGGGGGCGTGGGGGGTTGCCGCGGGCGGGGTCGCCGGCCGCTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTTGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATcc                                           <  4:8103/135‑1 (MQ=255)                                                                                             cctgggCGTGCACTCGGCGGGGGGGGTGTTGGCGGGGGCGGGGTCGCGGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATcc                                           <  3:188288/134‑1 (MQ=255)                                                                                                      ccACCAGGCGCGCGGGGTGTTGCCGCGGGCCGGCGCGCGGGCCCGTCAGCTGCGCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTAc                                  <  1:325185/136‑1 (MQ=255)                                                                                                       cACCCGGCGCGGTGGGGGTGGCCGGGGGCCGGCGCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACt                                 <  7:201223/137‑1 (MQ=255)                                                                                                       cACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCGCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACt                                 <  2:440586/137‑1 (MQ=255)                                                                                                        aCCAGGCGCGCTGGGTGTTGCCGCGGGGCGGCGCGCCGGCCCCGGCCCGGCGCGCCCACCGCCTCGCCCCCCCCGGCCGGCCCGCGCCCGGGCGGGGGGGGGGGACCGCTGGGCTGGCGGGTTTTCGTGGCCGAcgg                                >  8:457746/1‑135 (MQ=255)                                                                                                               gcgcTGGGTGTTGCCGCGGGCTGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACTGGTGCGtt                         >  6:306590/1‑137 (MQ=255)                                                                                                                 gcgggttgtTGCCGCGGGCGGGGTCGCCGGCGCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACTGGTGCGTTCg                       <  2:390380/131‑1 (MQ=255)                                                                                                                                    cGGCGCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACTGGTGCGTTCGGACATGCTGGCGGCGgtgt    <  2:329344/137‑1 (MQ=255)                                                                                                                                      gCTGGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGTCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACTGGTGCGTTCGGACATGCTGGCGGCGGTGTCt  <  7:378574/137‑1 (MQ=255)                                                                                                                                        |                                                                                                                                       GCCAGCGACCTGGTGGGCGAGCCGCTCATCAACGAGGAAATGGTGGTGCTGGCCCGTCGGGGGCACCCGCTGTTGCACACTCACCTGACGCTCAAGGGCGTGCACCAGGCGCGCTGGGTGTTGCCGCGGGCCGGCTCGCCGGCCCGTCAGCTGCTCGACAACTGCTTCGCCGCCGCGGGCCTGACAGCGCCGTGGCCGGTGGTGGAAAGCGCTGATCTGGCGGTTATCCGTGGCCTACTGGTGCGTTCGGACATGCTGGCGGCGGTGTCT  >  KT2440/2856751‑2857020

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑