Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,676,106	0	C	A	40.7%	33.5 / 11.1	27	L240F (TTG→TTT)	yphD	putative sugar ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base C (15/1);  new base A (0/11);  total (15/12)
Fisher's exact test for biased strand distribution p-value = 9.20e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAGCGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATG  >  NC_000913/2675956‑2676253                                                                                                                                                       |                                                                                                                                                    tAGCGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCcaac                                                                                                                                                     >  1:310671/1‑151 (MQ=255)    cGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCcaacaa                                                                                                                                                   >  2:322086/1‑150 (MQ=255)                          aaTGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCtaat                                                                                                                             >  1:568289/1‑150 (MQ=255)                                 cGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTCCCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCg                                                                                                                      >  2:139373/1‑150 (MQ=255)                                        ggAACCGCGACCGCCGGAAAGAGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGt                                                                                                               >  2:450995/1‑150 (MQ=255)                                                  ccgccgGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACCCCAGCCCGTTTGCGGCCCCTGCGTTCCCAGACCCGAGGCGCGCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGaa                                                                                                    <  1:364548/151‑1 (MQ=255)                                                  ccgccgAAAAGTGCCGTCCCGCCGCCCACGCCCGCGGCGATGACGTCAAACCCCAGCCCGTTTGCGGCCCCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATaa                                                                                                       <  1:447169/148‑1 (MQ=255)                                                      cgGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATgcg                                                                                                >  1:576355/1‑151 (MQ=255)                                                         aaaGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCAc                                                                                             >  1:405369/1‑151 (MQ=255)                                                             tGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCcg                                                                                          >  2:303258/1‑150 (MQ=255)                                                               ccgccccgccgACCCCGCCCGGGGCGAGGACGTCAAACCCCAGACCGTTGGCGGCCCCTGCGTTACCAGACCCGAGGCGCGCCGCAAAAAAAAGGCCGGTCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAATAATGCGCACCcga                                                                                         <  2:87307/144‑1 (MQ=255)                                                               ccGTCCCCCCGCCCCCGCCCGGGGCGAGGACGACAAACCCCAGCCCGTTTGCGGCCCCGGCGTTCCCAGAACCGGGGCGCGCCGCCAAAAAAAGGCGGGCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCcgacg                                                                                       <  2:3475/151‑1 (MQ=255)                                                                     cgccgcCCCCGACCGCGGCGATGACGCCAAACCCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAAc                                                                                    <  2:167899/148‑1 (MQ=255)                                                                       ccgACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTg                                                                                >  1:121045/1‑150 (MQ=255)                                                                              cgcccGCGGCGATGACGTAAAACTCCAGCCCTTTGCCGGCCCCTGCGTTACCAAAACCGAGGCGCGCCGCAAAAAAAATGCCGGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCg                                                                          <  2:384124/146‑1 (MQ=255)                                                                                 ccGCGGGAATAACGGCAACCCCCGGACCGTGTGCGGCACCTGCGTCACGAAATCCGAGGCGCGCCGCAAAAAAAAGCCGGGCCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGc                                                                         <  2:142395/147‑1 (MQ=255)                                                                                 ccGCGGCGAGGACGTCAACCCCCAGACCGTTGGCGGCCCCTGCTTTACCAGAACCGGGGCGCGCCGCAAAAAAAAGGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGc                                                                         <  2:102954/147‑1 (MQ=255)                                                                                  cgcgGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAAc                                                                    >  2:604407/1‑151 (MQ=255)                                                                                    cggcgATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTg                                                                  >  1:167250/1‑151 (MQ=255)                                                                                           gACTTCAACCGCCGGACCGTGTGCGGCCCCGGCGGTACCAGAACCGAGGCGCGCCGCCAAAAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACGGcgccgcg                                                           <  2:193100/151‑2 (MQ=255)                                                                                                 aaaCTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGc                                                      >  2:293616/1‑150 (MQ=255)                                                                                                       cAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCg                                               >  2:80215/1‑151 (MQ=255)                                                                                                                      ccttgggaccccAGAACCGGGCGGCGCCCACAAAAAAGGCCCGCTCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTGGCATTACCGCCAACGGCaa                                     <  2:384391/136‑1 (MQ=255)                                                                                                                                ccAGACCCGAGGCGCGCCGCAAAAAAAATCCCGGCCCCCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGa                      <  1:524422/151‑1 (MQ=255)                                                                                                                                    aaCCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGc                  >  1:412224/1‑151 (MQ=255)                                                                                                                                      ccGAGGCGGCCCGCAAAAAAAAGGCCGTTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGc                  <  1:160266/149‑1 (MQ=255)                                                                                                                                         aGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAGGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAACAACCGAGCGCCCGAAGGCGGttt             >  2:394347/1‑151 (MQ=255)                                                                                                                                         aGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGTGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGttt             >  1:512171/1‑151 (MQ=255)                                                                                                                                                ccgccAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCg         >  2:7492/1‑148 (MQ=255)                                                                                                                                                ccccaaacaaATTCCCGTTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCt      <  1:89959/146‑1 (MQ=255)                                                                                                                                                    caacaaAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCtgatg  >  2:444138/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                    TAGCGTAATCACCAGCACACCAAGCAATGTACCGAACAGGGAACCGCGACCGCCGGAAAGTGCCGTACCGCCGACCACGACCGCGGCGATGACGTCAAACTCCAGACCGTTTGCGGCACCTGCGTTACCAGAACCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATG  >  NC_000913/2675956‑2676253

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: ‑