Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	71,566	0	C	T	50.0%	4.3 / 11.3	16	L134L (CTG→CTA)	thiB	thiamine ABC transporter substrate binding subunit
Reads supporting (aligned to +/- strand):  ref base C (0/8);  new base T (8/0);  total (8/8)
Fisher's exact test for biased strand distribution p-value = 1.55e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: E-value score below prediction cutoff.
Rejected as consensus: Frequency below/above cutoff threshold.

TTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTG  >  NZ_CP009273/71451‑71677                                                                                                                    |                                                                                                                tttGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTCTTGTCATAAACg                                                                                            >  2:357036/1‑137 (MQ=255)   tGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAg                                                                                         <  1:323045/138‑1 (MQ=255)             gCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGc                                                                               <  1:33561/138‑1 (MQ=255)                             cGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTCGTTTTTTTTTTTCATAAAAGAAAGCGAAGGAGGCATAATTAAAAGGTAc                                                               >  1:592092/1‑138 (MQ=255)                                       gTGCGCGGTTCCTTATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCa                                                     <  1:397247/138‑1 (MQ=255)                                          cgcgGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTCTGTTGTTTTTGTTATAAACAAAGGCGGAGGAGCCCTAATCAAAAAGTTCGAAAGTGTTatttt                                                 >  2:287996/1‑137 (MQ=255)                                          cgcgGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTATTTTTTTTTTTTTATAAACCAAAGCGGAGGAGCCATAATCAAACGGGACGAAAGTGTCattat                                                 >  1:429423/1‑139 (MQ=255)                                          cgcgGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTAGTTTGTTCTTGTCATTAACGAAGGGGAAGTAGCCATAAACAAACGGGACGAAAGAGTCcttat                                                 >  1:164305/1‑139 (MQ=255)                                            cgGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTTTGTTTTTTTTTGTCATAAAACAAGGGGAAGGAGGCCAAATCAAACGGGACCAAAACATCattattt                                               >  2:661126/1‑138 (MQ=255)                                                 ccTGAAAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAgcc                                          <  2:327539/139‑1 (MQ=255)                                                     aTAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGccgccg                                      <  1:383688/139‑1 (MQ=255)                                                     aTAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTTTTTTTGTCATAAACGAAGGCGGAGGAGCCCTAATCAAACGGTACGAAAGTGTCATTATTTCAgccgccc                                      >  2:138513/1‑138 (MQ=255)                                                       aaaTCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCggg                                    <  2:298219/139‑1 (MQ=255)                                                               cGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTaa                            <  2:485313/139‑1 (MQ=255)                                                                   aGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGc                        <  2:560973/139‑1 (MQ=255)                                                                                         ttCTTTCAGGCTTTGTGGCGGGGTTTTTTGTTTGGTTTTGTCTTTAACGAAAGCGGAGGAGGCCGAATCAAAACGGAAGAAAATGTCATTATTCCAGCCGCCGGGGACGCTAAAGGCCCCTCCTCCCACACCGCctttt  >  1:44070/1‑138 (MQ=255)                                                                                                                    |                                                                                                                TTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTG  >  NZ_CP009273/71451‑71677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑