Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,676,186	0	A	G	23.5%	88.7 / 26.5	51	L214L (TTG→CTG)	yphD	putative sugar ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base A (20/19);  new base G (5/7);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 7.43e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

CCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAAACAACACAATCA  >  NC_000913/2676089‑2676281                                                                                                  |                                                                                                ccGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACt                                                                                               >  2:1257837/1‑100 (MQ=255)  cGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTg                                                                                              >  2:1293421/1‑100 (MQ=255)     ggCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAGCTgcgc                                                                                           <  2:1090996/100‑1 (MQ=255)       cgcgcCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGcgccg                                                                                         >  1:1014088/1‑100 (MQ=255)         cgccgcCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCgccgcc                                                                                       <  2:823861/100‑1 (MQ=255)           ccgccAACAAAATGCCGGTCACCGCCGCTAATAAGCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGt                                                                                     <  2:1165883/100‑1 (MQ=255)            cgccAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTa                                                                                    <  1:528126/100‑1 (MQ=255)            cgccAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTa                                                                                    <  2:1186477/100‑1 (MQ=255)              ccAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGc                                                                                  <  2:443267/100‑1 (MQ=255)               caacaaAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCa                                                                                 >  1:637211/1‑100 (MQ=255)                  caaAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTa                                                                              >  2:1225043/1‑100 (MQ=255)                       tGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGcc                                                                         <  2:152089/100‑1 (MQ=255)                        gCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGc                                                                          <  1:739248/98‑1 (MQ=255)                         ccGGTCACCGCCCCGAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCaa                                                                       >  2:760206/1‑100 (MQ=255)                          cGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAAc                                                                      >  2:919345/1‑100 (MQ=255)                             tCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCAGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGc                                                                   <  1:918801/100‑1 (MQ=255)                                ccgccgCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCaaa                                                                >  1:418116/1‑100 (MQ=255)                                ccgccgCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCaaa                                                                >  1:651804/1‑100 (MQ=255)                                        aataatCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACAGCAAAAACCGa                                                          >  2:175686/1‑98 (MQ=255)                                           aatCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGcc                                                     >  2:1232015/1‑100 (MQ=255)                                              cccGAAGGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTAACGCCAACAGAAAAAACCGAGCGCCCGa                                                  <  2:1035775/100‑1 (MQ=255)                                                cGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAg                                                >  2:544796/1‑100 (MQ=255)                                                    atgatAAAGATAAGCTTGCGCACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCgg                                            <  2:722709/96‑1 (MQ=255)                                                     gggTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGt                                           >  1:1048539/1‑100 (MQ=255)                                                     gggTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGt                                           <  1:1064842/100‑1 (MQ=255)                                                     gggTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAAGCgg                                            >  2:921038/1‑99 (MQ=255)                                                      ggTAAGGATAAGAATGCGCACGCGATGAACGTTGATGCCGGACAACTGCGCAGGCGTAGGATTAGGGCAAACGGCAAAAACCGAGCGCCCGAAGGTGGtt                                          >  2:1084152/1‑100 (MQ=255)                                                      ggTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCACCGGCAAAAACCGAGCGCCCGAAGGCgg                                            >  2:904441/1‑98 (MQ=255)                                                           aGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCg                                     <  2:948869/100‑1 (MQ=255)                                                              tAAGAATGCGCACCCGACGAACGTTGATTCCGCACAAATGCGCCGCCCTACCATTACCGCCACCCGCAAAAACCGAGCGCCCGAAGGCggctatccg                                     >  2:105956/1‑90 (MQ=255)                                                              tAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCt                                  >  1:808627/1‑100 (MQ=255)                                                                  aaTGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCtgatg                              >  2:902545/1‑100 (MQ=255)                                                                     gcgcACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAac                           >  2:594906/1‑100 (MQ=255)                                                                      cgcACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAaca                          >  2:1196449/1‑100 (MQ=255)                                                                       gcACCCGACGAACGTTGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAaca                          <  2:539917/99‑1 (MQ=255)                                                                        cACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAAcaca                        <  1:473680/100‑1 (MQ=255)                                                                           ccGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAAc                     <  1:103778/100‑1 (MQ=255)                                                                           ccGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAAc                     <  2:612480/100‑1 (MQ=255)                                                                            cgacgaACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACa                    >  2:651628/1‑100 (MQ=255)                                                                                  aCGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCaa              <  1:596207/100‑1 (MQ=255)                                                                                   cGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCaaa             <  2:501905/100‑1 (MQ=255)                                                                                     ttGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAaaca           <  2:1945/100‑1 (MQ=255)                                                                                     ttGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAaaca           <  1:1257848/100‑1 (MQ=255)                                                                                     ttGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCCAGCGCCCGAAGGCGGCTTTGCGGCTGATGAACACAAACAGCGCAaaca           >  2:185915/1‑100 (MQ=255)                                                                                      tGATGCCGCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAaaca           <  2:1281686/99‑1 (MQ=255)                                                                                        aTGCCGAACAGCTGCGCCGCCGTAGCATTAAAAAAAAAAAAAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGACGAACACAAACAGCGCAaacaac         <  2:758016/99‑1 (MQ=255)                                                                                         tGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAAACAacac       >  2:1053786/1‑100 (MQ=255)                                                                                         tGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAAACAacac       <  1:1293432/100‑1 (MQ=255)                                                                                             gCACAGCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTCCGGCTGATGAACACAAACAGCGCAAACAACACaa     >  2:1139986/1‑98 (MQ=255)                                                                                             gCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAAACAACACAATc   <  1:1232026/100‑1 (MQ=255)                                                                                              cacaACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAAACAACACAATCa  <  1:389672/100‑1 (MQ=255)                                                                                                 aaCTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCTAGCGCCCGAAGGCGGTTTTACGGCTGAAGAACACAAACAGCGCAAACAACACAATCa  >  2:1171386/1‑97 (MQ=255)                                                                                                  |                                                                                                CCGAGGCGCGCCGCCAACAAAATGCCGGTCACCGCCGCTAATAATCCCGAAAGGGTAAAGATAAGAATGCGCACCCGACGAACGTTGATGCCGCACAACTGCGCCGCCGTAGCATTACCGCCAACGGCAAAAACCGAGCGCCCGAAGGCGGTTTTGCGGCTGATGAACACAAACAGCGCAAACAACACAATCA  >  NC_000913/2676089‑2676281

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑