Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	75,079	0	C	T	59.3%	5.2 / 30.7	27	L134L (CTG→CTA)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base C (0/11);  new base T (16/0);  total (16/11)
Fisher's exact test for biased strand distribution p-value = 7.67e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.09e-05

CTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAAC  >  NC_000913/74937‑75223                                                                                                                                               |                                                                                                                                                 cTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTtgtttgtt                                                                                                                                          >  2:501659/1‑151 (MQ=255)           gTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTTTTTTTTTCCTaa                                                                                                                                >  1:111165/1‑151 (MQ=255)             cATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAAc                                                                                                                              <  2:337590/151‑1 (MQ=255)             cATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAAc                                                                                                                              <  1:410953/151‑1 (MQ=255)               tCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGa                                                                                                                            <  1:375402/151‑1 (MQ=255)                 gCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTGTTTTTTTTATAAaagaag                                                                                                                          >  1:187346/1‑151 (MQ=255)                                        gCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTCTTTTCATAAAAGAAGGGGAAGTAGCCATAATCAAACgg                                                                                                   >  1:430350/1‑151 (MQ=255)                                             aGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGGTTTTTCTTGTCCTAAAAGAAGGCGGAGAAGACATAATCAAACCGGACGa                                                                                              >  1:307940/1‑151 (MQ=255)                                              gACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTTTTTTAAAAAAAAGGGAAGGAGACCTAATCAAACgggaggga                                                                                             >  2:507072/1‑145 (MQ=255)                                               ccccAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGaa                                                                                             <  2:383412/149‑1 (MQ=255)                                                cccAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAg                                                                                           <  2:164939/151‑1 (MQ=255)                                                    gCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTTTTCTTTTTATAAACGAAGGCGAAGAAGCCCTAATCAAAAGGGACGAAAgtgt                                                                                        >  1:44417/1‑150 (MQ=255)                                                    gCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTTTTATAAAAGAAGGCGAAGGAGCCAAAATAAAACAGTACGAAAgggt                                                                                        >  1:368073/1‑150 (MQ=255)                                                          gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTTTTCTTTTCATAAAACAAGGCGGAATAGCCATAATCAAAAGGTAAGAAAGAGTCattttt                                                                                 >  1:285640/1‑151 (MQ=255)                                                           tgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTc                                                                                <  1:325406/151‑1 (MQ=255)                                                            gtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTTATAAACCAAGGCGGAGTGGGCCTAATCAAACGGGTCGCAAGTGTTattattt                                                                                >  2:486742/1‑149 (MQ=255)                                                            gtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTTTTTTCATAAAAGAAAGCGGAGTAGGCATAATCAAACGGGACGAAAATGTCattattt                                                                                >  1:244900/1‑149 (MQ=255)                                                                                aTAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACg                                                           <  1:156865/151‑1 (MQ=255)                                                                                 aaaaTCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACgg                                                          <  2:100400/150‑1 (MQ=255)                                                                                          cGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTCATAAAAGAAGGGGAAGGAGCCATAATTAAACGGTACGAAAGTGTCATTTTTTCAGCCGCCCGGAACGGTAAAGGCAACCGccg                                                 >  2:541332/1‑149 (MQ=255)                                                                                               gTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTTTTTTTTTCATAAACGAAAGCGGAGTAGGCATAATTAAACGGTACGAAAGTGTCATTTTTTCAGCCGCCGGGAACGTTTACGGCATCCGCCGCccca                                            >  1:352823/1‑151 (MQ=255)                                                                                                ttttGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCacac                                           <  1:394952/151‑1 (MQ=255)                                                                                                             cAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTAGTTTGTTTTTTTCATAAAAGAAGGCGAAGTAGCCATAATCAAACGGGACGAAAGGGTCATTTTTCCAGCCGCCGGGGACGTTAAAGGCATCCCCTGCCACACCGCTTTTTGCaaa                              >  1:326567/1‑151 (MQ=255)                                                                                                             cAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGGTTTTTTTTTTTATAAACGAAGGCGAAGGAAGCCTAATAAAAACGGAAGAAAATGTTATTATTCCAACCGCCCGGGAAGTTTACGGCAACCGCTGCCCCACCCCCTTTTGTaaa                              >  1:227181/1‑151 (MQ=255)                                                                                                                   gTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTTTTATAAAAGAAGGCGAAGGAGGCATAATCAAAAGGTACGAAAATGTCATTATTTCAGCCGCCGGGGACGTTAACGGCATCCCCCGCCCCACCCCTTTTTGCCAACaagc                         >  2:603213/1‑147 (MQ=255)                                                                                                                     tCTTCCAGGTTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAACCGAAGGCAAATTGGCCATAATAAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTG‑CACACCGCTTTTGGCAAACAGTCCGGt                     <  1:234500/151‑1 (MQ=255)                                                                                                                                          tttttCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAAc  <  2:302848/150‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                 CTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAAC  >  NC_000913/74937‑75223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑