Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	701,009	0	T	A	52.4%	7.6 / 23.7	21	I537N (ATC→AAC)	nagE	PTS N‑acetyl glucosamine transporter subunit IIABC
Reads supporting (aligned to +/- strand):  ref base T (2/8);  new base A (11/0);  total (13/8)
Fisher's exact test for biased strand distribution p-value = 2.21e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.50e-03
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

ATGTCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCAACACCAACCACGCGTTCTGCCTGGAAACCGAAAAAGGCGCGGAGATC  >  NZ_CP009273/700922‑701097                                                                                        |                                                                                         aTGTCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAAtcg                                                                                        <  2:1164038/90‑1 (MQ=255) aTGTCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAAACGACAGATAAAGtcg                                                                                        >  2:164466/1‑90 (MQ=255)    tCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAAtcgtcg                                                                                     <  2:641229/90‑1 (MQ=255)    tCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAAtcgtcg                                                                                     <  2:390811/90‑1 (MQ=255)    tCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAAtcgtcg                                                                                     <  1:862971/90‑1 (MQ=255)             tGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGGAAACGGCAGATAAAAACGTCGGATCACCAg                                                                            >  1:860694/1‑90 (MQ=255)                   aGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAAACGTCGGATCACCAGcccccg                                                                      >  2:1370722/1‑86 (MQ=255)                        ccTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGGGGAAACGACAGATAAAAACGTCGGATCACCAGCCGCAggggga                                                                 >  1:42624/1‑87 (MQ=255)                          tGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAAACGACAGATAAAAACGTCGTATCACCAGCCGCAGGGGCAAt                                                               >  2:1167368/1‑90 (MQ=255)                              gAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGGGAAACCGACAGATAAAATCGGCGTATCACCAGCCGCAGGGGCAATCggg                                                           >  2:515717/1‑88 (MQ=255)                                  cATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGaaaa                                                       <  1:280886/90‑1 (MQ=255)                                       gCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTc                                                  <  2:1247131/90‑1 (MQ=255)                                        ccAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCa                                                 <  2:995366/90‑1 (MQ=255)                                        ccAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCa                                                 <  2:971127/90‑1 (MQ=255)                                           gCAAAGCGGTGGGTGACGGTGTGGCGGGGAAAACGACAGATAAAATCGTCGTATCACCAGCCGCCGGGGCAATCGGGAAAAAATTCaaaa                                              >  2:660265/1‑88 (MQ=255)                                                   gtgggtgACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCAACACCAACCAc                                      <  1:584390/90‑1 (MQ=255)                                                     gggtgACGGTGTGGCGGGGAAAACGACAGATAAAAACGTCGTATCACCAGCCCCAGGGGGAAACGGGAAAAAATTTAAAACCcaccaccc                                    >  1:96769/1‑88 (MQ=255)                                                             gtgtGGCGGTGAAAACGACAGATAAAAACGTCGTATCACCAGCCGCAGGGGCAAACGGGAAAAACTTCAAAACCAACCACGCGGTCTGcc                            >  2:1291354/1‑90 (MQ=255)                                                               gtgGCGGTGAAAACGACAGATAAAAACGTCGTATCACCAGCCGCAGGGGGAATCGTGGAAAAATTCAACACCAAACACCCGCTCTGCCTg                          >  1:627195/1‑90 (MQ=255)                                                               gtgGCGGTGAAAACGACAGAAAAAAAAGTCGTATCACCAGCCGCAGGGGCAAACGGGAAAAACTTCAACACCAACCACCCGTTCTGCCTg                          >  1:816693/1‑90 (MQ=255)                                                                 ggCGGTGAAACCGACAGGTAAAAAAGTCGTATTACCAGCCCCCGGGGGAAACGTGGAAAACTTCAACACCCACCACCCGTTCTGCCTggg                        >  1:1434425/1‑89 (MQ=255)                                                                 ggCGGTGAAAACGACAGATAAAAACGTCGTATCACCAGCCGCAGGGGCAATCGGGAAAAAATTCAAAACCAACCACGCGTTCTGCCTGGa                        >  1:521894/1‑90 (MQ=255)                                                                   cGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCAACACCAACCACGCGTTCTGCCTGGaaa                      <  1:1358570/90‑1 (MQ=255)                                                                       gAAAACGACAGATAAAAACGTCGTATCACCAGCCGCAGGGACAATCGTGAAAAACTTCAACACCAACCCCGCGTTTTGCCTTGGAAccca                  >  2:945406/1‑88 (MQ=255)                                                                           ccGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCAACACCAACCACGCGTTCTGCCTGGAAACCGaaaaa              <  1:356466/90‑1 (MQ=255)                                                                                      aaTCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCAACACCAACCACGCGTTCTGCCTGGAAACCG‑AAAAGGCGCGGAGAtc  <  1:469307/90‑1 (MQ=255)                                                                                        |                                                                                         ATGTCGTGGCACTGGATCAGGTTCCTGACGAAGCATTCGCCAGCAAAGCGGTGGGTGACGGTGTGGCGGTGAAACCGACAGATAAAATCGTCGTATCACCAGCCGCAGGGACAATCGTGAAAATCTTCAACACCAACCACGCGTTCTGCCTGGAAACCGAAAAAGGCGCGGAGATC  >  NZ_CP009273/700922‑701097

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑