Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	579,146	0	A	G	55.0%	2.3 / 14.7	20	intergenic (‑253/+38)	borD/ybcV	prophage lipoprotein BorD/DUF1398 domain‑containing protein YbcV
Reads supporting (aligned to +/- strand):  ref base A (8/1);  new base G (6/5);  total (14/6)
Fisher's exact test for biased strand distribution p-value = 1.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

CCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCGTGGATATTTGTAATCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGATTTCAACCTATCATAGGACGTTTCTATAAGATGCGTATTTCTT  >  NC_000913/578903‑579391                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      cccGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTg                                                                                                                                                                                                                                               >  1:8287/1‑251 (MQ=255)              gAAGTTCGCAGAATCGTATGAGTAGAAAATTAACCAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGga                                                                                                                                                                                                                                     >  1:209200/1‑249 (MQ=255)                                   gtAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGGGCTGACACGGAAGAAACCGGACGTTATGATTTAGc                                                                                                                                                                                                             >  1:13407/1‑251 (MQ=255)                                   gtAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTa                                                                                                                                                                                                               >  1:208984/1‑250 (MQ=255)                                                         atcAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGTCAGGTGCGATGAATCGTCATTGTATTCCCTGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAgtgtn                                                                                                                                                                                       <  1:157813/249‑2 (MQ=255)                                                                                                 gTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGt                                                                                                                                                >  1:213552/1‑251 (MQ=255)                                                                                                              gATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGCGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑TGATGCACACAGGGTTTAGCGCGTACACGTATTGAATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCttt                                                                                                                                  >  1:193164/1‑251 (MQ=255)                                                                                                                      gTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGAGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGATACCGGACGTTCTGATTTAGCGAGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTCTCAAAGGTATAGTAATATCTTTTATGTTc                                                                                                                           >  1:242182/1‑251 (MQ=255)                                                                                                                                              tGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTTTCCGGGAATAAGTAAAA‑CTGGGCACACAGGGTTTAGCGCGTACACGTGTTGCATCATGCTAACGGCGCGGTGCTGTCACGGAAGAATCCGGACGTTATGATTTAGCGTGGAAAGAtt                                                                                                                                                                                                  <  1:236024/155‑1 (MQ=255)                                                                                                                                               gTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAGACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACACCGGAGCTGACACGGAGGAAACCGGACGTTATGATTTAGCGTGGTCAGATTTGTGGAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTAGTGGAAATTTGTAATCCATCGGaa                                                                                                   >  1:243239/1‑250 (MQ=38)                                                                                                                                                         cTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGCATACTTACAAACGATGCACACCGGGATTCGCGCGTAGCTGTATTGTATTATGCAAACACCCCGCTGCTGACCCGGCAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGCAGTGTTCTGAATGCTCTCAGTAAATAGAAATGAATTATCAAAg                                                                                                                                                  >  1:100061/1‑193 (MQ=255)                                                                                                                                                                   aCTTCTCTGCGGGAGTGTCCGGGAATAATTAAAA‑CGATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGATGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTGATGTTCATGGATATTTGTAACCCATCGGAAAACTCCTGCTTTAGCAAGAttt                                                                             <  1:141574/251‑1 (MQ=37)                                                                                                                                                                                   gtCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCa                                                                                                                                                                          >  1:2212/1‑143 (MQ=255)                                                                                                                                                                                      cGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAacac                                                                                                                                                                                                                                                      >  1:193578/1‑64 (MQ=255)                                                                                                                                                                                      cGGGAATAATTAAAA‑CGATGCGCACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTAGAGTAATATCTTTTGGGTTCATGTATATTGGTAACCCATCGGAAAACGCCTGCTTTAGCAAGATTTTCCCTGTATTGCTGAAAtg                                                          <  1:114171/251‑1 (MQ=25)                                                                                                                                                                                        ggAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGCAACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGaa                                                                                                                                                           >  1:130676/1‑153 (MQ=255)                                                                                                                                                                                                       gATGCACACAGGGTTTAGCGCGTACACGTATTGCATTATGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGCTTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTATCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCATGGATATTTGTAACCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGAttt                                          >  1:222092/1‑251 (MQ=25)                                                                                                                                                                                                                                      tgtattATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCGTGGATATTTGTAATCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGATTTCAACCTATCATAGGACGTTTCTATAAGATg            <  1:78934/250‑1 (MQ=255)                                                                                                                                                                                                                                       gcattatGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCATGGATATTTGTAACCCATCGGAAAACTcc                                                                                             <  1:234218/166‑1 (MQ=255)                                                                                                                                                                                                                                        cattatGCCAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAata                                                                                                                                       >  1:17179/2‑125 (MQ=255)                                                                                                                                                                                                                                               ccAACGCCCCGGTGCTGACACGGAAGAAACCGGACGTTATCATTTAGCGTGGAACGATCTGCGTAGTGTTCTGAATGCTCTCAGTAAATAGTACTGAATTATCAAAGGTATAGTAATATCTTTTATGTTCATGGATATTTGTAACCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGATTTCAACCTATCATAGGACGTTTCTATAAGATGCGTGTTTCtt  >  1:233521/1‑251 (MQ=25)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      CCCGATGCTTTTTGAAGTTCGCAGAATCGTATGTGTAGAAAATTAAACAAACCCTAAACAATGAGTTGAAATTTCATATTGTTAATATTTATTAATGTATGCCAGGTGCGATGAATCGTCATTGTATTCCCGGATTAACTATGTCCACAGCCCTGACGGGGAACTTCTCTGCGGGAGTGTCCGGGAATAATTAAAAACGATGCACACAGGGTTTAGCGCGTACATGTATTGTATTATGCCAACACCCCGGTGCTGACACGGAAGAAACCGGACGTTATGATTTAGCGTGGAAAGATTTGTGTAGTGTTCTGAATGCTCTCAGTAAATAGTAATGAATTATCAAAGGTATAGTAATATCTTTTATGTTCGTGGATATTTGTAATCCATCGGAAAACTCCTGCTTTAGCAAGATTTTCCCTGTATTGCTGAAATGTGATTTCTCTTGATTTCAACCTATCATAGGACGTTTCTATAAGATGCGTATTTCTT  >  NC_000913/578903‑579391

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑