Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,472,581	0	T	G	52.9%	13.3 / 24.2	17	G33G (GGT→GGG)	ynbB	phosphatidate cytidylyltransferase
Reads supporting (aligned to +/- strand):  ref base T (1/7);  new base G (9/0);  total (10/7)
Fisher's exact test for biased strand distribution p-value = 4.11e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.24e-03
Rejected as consensus: Frequency below/above cutoff threshold.

TTGTCGGAGTGTGCTTCTTATGAGCGCTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTGTTTTTCAATGGTGATTTCAGGTCCACGCTGGATGACGTTGACGTTTTTTGCGCTGATAAGTTTTCTGGCATTGAAAGAATATTGT  >  NZ_CP009273/1472447‑1472710                                                                                                                                       |                                                                                                                                  ttGTCGGAGTGTGCTTCTTATGAGCGCTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGTGAgg                                                                                                                               <  2:461467/139‑1 (MQ=255)            tgCTTCTTATGAGCGCTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGTGAGGTTACATTACg                                                                                                                     <  2:15155/138‑1 (MQ=255)                 cttATGAGCGCTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGTGAGGTTACATTACGTAtt                                                                                                                 <  2:26955/137‑1 (MQ=255)                         cgcTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGGGAGAAAAGGGGGt                                                                                                                                   >  2:198491/1‑111 (MQ=255)                         cgcTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGt                                                                                                                                   <  1:198491/111‑1 (MQ=255)                           cTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAACAGGGGGGGGGGTTACATTATGTATTCGTACCttgtgg                                                                                                     >  2:152467/1‑139 (MQ=255)                                      tGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGGGGGAAAAGGGGGGGGGGGTACATTACGTATTTGTAACTGGGGGGGGATCGGCAt                                                                                          >  1:196252/1‑139 (MQ=255)                                        cTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGGGGGAAAAGGGGGGGAGGGTAGCATACGGAATCCTACCCGGTGGGGGGTCGTCAttt                                                                                        >  1:144677/1‑139 (MQ=255)                                           gAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTTTCGGAGAGAAAAGGGGGGGAGGGTACATTACGTATTCGGACCTGGTGGGGCATCGTCAtttttt                                                                                     >  2:313729/1‑139 (MQ=255)                                           gAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTg                                                                                       <  2:55153/137‑1 (MQ=255)                                                           cacTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGTGAGAAAAGGGGGGGGGGGTAACTTTCGTATTCGGACCGGGTGGGGGATCGGCCTTTGTTTTTTAATGGTGAtttg                                                                     >  2:228575/1‑138 (MQ=255)                                                                 tCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTAACGGAGAGAAAAAGGGGGGGGGGTACATTACGTATTTGTTCCTGGTGGGGGGTCGTCATTTGTTTTTTTATGGTGATTTTCGGTcc                                                               >  1:53255/1‑139 (MQ=255)                                                                        gttAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGGGAGAAAAGGGGGGGGGGGTACATTACGTATTTGTACCTGGGGGGGGGTCGTCATTTGTTTTTTTATGGGGGTTTTTGGTCCACGCTgg                                                        >  2:64852/1‑139 (MQ=255)                                                                                   cAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGGGAAAAAGGGGGGGGGGTTCATTACGTATTCGTACCTGGTGGGGGATCGTCATTTGTTTTTCAATGGTGATTTCAGGTGCACGCCGGGtggcgttgac                                             >  2:321907/1‑139 (MQ=255)                                                                                                ccGTTTTCTGCTATGGCGGTTTTCGGGGAGAAAAGGGGGGGAGGGTTAATTACGTTTTTTTTCCTTGTGGGGGGTCGTCATTTTTTTTTTAATTGTGTTTTTTGGTCCACGCTGGGTGACGGTTACGTTTTTTTTGCTg                                >  1:480636/1‑139 (MQ=255)                                                                                                                         gagagaAAAGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTGTTTTTCAATGGTGATTTCAGGTCCACGCTGGATGACGTTGACGTTTTTTGCGCTGATAAGTTTTCTGGCATTGAAAGaa        >  1:9728/1‑138 (MQ=255)                                                                                                                              aaaaGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTGTTTTTCAATGGTGATTTCAGGTCCACGCTGGATGACGTTGACGTTTTTTGCGCTGATAAGTTTTCTGGCATTGAAAGAATATTGt  <  2:357152/139‑1 (MQ=255)                                                                                                                              aaaaGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTGTTTTTCAATGGTGATTTCAGGTCCACGCTGGATGACGTTGACGTTTTTTGCGCTGATAAGTTTTCTGGCATTGAAAGAATATTGt  <  2:480636/139‑1 (MQ=255)                                                                                                                              aaaaGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTGTTTTTCAATGGTGATTTCAGGTCCACGCTGGATGACGTTGACGTTTTTTGCGCTGATAAGTTTTCTGGCATTGAAAGAATATTGt  <  2:53255/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                  TTGTCGGAGTGTGCTTCTTATGAGCGCTGAAATATAATGCTGGAAAAATCTCTGGCAACACTTTTCGCGTTGTTAATTTTAGCAACGCTGATAAACCGTTTTCTGCTATGGCGGTTACCGGAGAGAAAAGGGGGTGAGGTTACATTACGTATTCGTACCTGGTGGGGCATCGTCATTTGTTTTTCAATGGTGATTTCAGGTCCACGCTGGATGACGTTGACGTTTTTTGCGCTGATAAGTTTTCTGGCATTGAAAGAATATTGT  >  NZ_CP009273/1472447‑1472710

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑