Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,751,893	0	G	A	60.0%	‑1.9 / 14.0	15	intergenic (‑25/‑99)	yiaT/yiaU	outer membrane protein YiaT/putative DNA‑binding transcriptional regulator YiaU
Reads supporting (aligned to +/- strand):  ref base G (2/4);  new base A (6/3);  total (8/7)
Fisher's exact test for biased strand distribution p-value = 3.15e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

GACAGAATAAAACCTAACGTGGTCTGACGAACATAAAAAGTATCACCTTCATAACTAATCAGCGGAATTGCCTTCGTATTTTCATTATAACCGCGATAAGGCGATTCATTATAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGTACCGGGAGTTAAAAATTATCTCGGTAATCGCTGCCAGTGAAAATATCAGCCATGCCGCGACTGTACTTGGCATCGCACAGGCCAACGTCAGCAAATATCTTGCTGAT  >  NC_000913/3751663‑3752120                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                    gACAGAATAAAACCTAACGTGGTCTGACGAACATAAAAAGTATCACCTTCATAACTAATCAGCGGGATTGCCTTCGTATTTTCATTATAACCGCGATAAGGCGATTCATTATAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATaaaaa                                                                                                                                                                                                                              >  1:307064/1‑238 (MQ=255)                            cGAACATAAAAAGTATCACCTTCATAACTAATCAGCGGAATTGCCTTCGTATTTTCATTATAACCGCGATAAGGCGATTCATTATAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCa                                                                                                                                                                                        >  1:117700/1‑249 (MQ=255)                                                            cAGCGGAATTGCCTTCGTATTTTCATTATAACCGCGATAAGGCGATTCATTATAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTTCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATtat                                                                                                                                                      >  1:21433/1‑251 (MQ=255)                                                                                 ttCATTATAACCGCGATAAGGCGATTCATTATAAGCCGCACCAGCACCAATGTATAATTCAGAAGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGAGTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGa                                                                                                                                  <  1:163155/250‑1 (MQ=255)                                                                                                 tAAGGCGATTCATTATAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGc                                                                                                                                                                                                           <  1:231453/161‑1 (MQ=255)                                                                                                 tAAGGCGANTNNNTNNAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTGCGCTTNCCATAAAAGGCAACGNAANTAACNCCANAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGc                                                                                                                                                                                                           >  2:231453/1‑161 (MQ=255)                                                                                                                                               aaGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGGGATTAATTAACATGGACGGTATTACATTTTAAACTAAGATACAAAAGAGTCGGCATAATAATGCTTACAATTTCTCAGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGc                                                                                                                                          >  1:168467/1‑180 (MQ=255)                                                                                                                                                    gTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGTACCGGGAGTTAAAAATTATCTCGGTAATCGCTGCCAGTGAAAatat                                                               >  1:270084/1‑250 (MQ=255)                                                                                                                                                                           cGCAAATAACGCCACAATAGTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCGGTTGCGATGAc                                                                                                                              <  1:180245/164‑1 (MQ=255)                                                                                                                                                                             cAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGt                                                                                                             >  1:3594/1‑179 (MQ=255)                                                                                                                                                                                                gCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGTACCGGGAGTTAAAAATTATCTCGGTAATCGCTGCCAGTGAAAATATCAGCCATGc                                                      <  1:591/215‑1 (MQ=255)                                                                                                                                                                                                gCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAAATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGANNCATATTnnt                                                                                                                                                                          >  2:591/1‑99 (MQ=255)                                                                                                                                                                                                          aaCATGTCCGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATGTAGATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGTACCGGGAGTTAAAAATTATCTCGGTAATCGCGGCCAGTGAAAAGATCAGCCGTGCCGCGTCTGTACTTGGCATCGCACAGGCCAACGTCAGCAAATATCtt        <  1:280389/251‑1 (MQ=255)                                                                                                                                                                                                                  cGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGTACCGGGATTTAAAAATTATCTCGGTAATCGCTGCCAGTGAAAATATCAGCCATGCCGCGACTGTACTTGGCATCGCACAGGCCAACGTCAGCAAATATCTTGCTGAt  <  1:273564/249‑1 (MQ=255)                                                                                                                                                                                                                                annaTAAAANNAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATCGGGc                                                                                                                                          <  2:21433/99‑1 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                    GACAGAATAAAACCTAACGTGGTCTGACGAACATAAAAAGTATCACCTTCATAACTAATCAGCGGAATTGCCTTCGTATTTTCATTATAACCGCGATAAGGCGATTCATTATAAGCCGCACCAGCACCAATGGATAATTCAGAAGCAGTTGCGCTTGCCATAAAAGGCAACGCAAATAACGCCACAATATTGCGATTAATTAACATGTCCGGTATTCCATTTTAAAATAAGATAAAAAAGAGTCGGCATAATAATGCTTACAATTTCTCCGGTGCAAGATTCATATTTATATAGTAATATATAAAATTATATATAATTGGGCTGTTGCGATGACAAAATTACAACTTAAGTACCGGGAGTTAAAAATTATCTCGGTAATCGCTGCCAGTGAAAATATCAGCCATGCCGCGACTGTACTTGGCATCGCACAGGCCAACGTCAGCAAATATCTTGCTGAT  >  NC_000913/3751663‑3752120

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑