Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,808,417	(A)8→9	intergenic (‑319/‑123)	waaQ ← / → waaA	lipopolysaccharide core heptosyltransferase 3/KDO transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,808,409	1	.	A	100.0%	61.9 / NA	18	intergenic (‑311/‑131)	waaQ/waaA	lipopolysaccharide core heptosyltransferase 3/KDO transferase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base A (10/8);  total (10/8)

AGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑AAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAGTCAAAAACGGGAAAAG  >  NC_000913/3808334‑3808476                                                                             |                                                                    aGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTTAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑aaaa                                                                 >  1:748544/1‑80 (MQ=255)  gCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑aaaaa                                                                >  1:748528/1‑80 (MQ=255)    aTTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑aaaaaaa                                                              >  2:748537/1‑80 (MQ=255)       tCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑aaaaaaaaat                                                           <  1:748510/80‑3 (MQ=255)         gATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑aaaaaaaaatg                                                          >  1:748530/1‑76 (MQ=255)           tAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGa                                                       <  2:748512/81‑1 (MQ=255)            aaTGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGAt                                                      >  1:748539/1‑81 (MQ=255)             aTGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATg                                                     >  1:748533/1‑81 (MQ=255)              tGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATg                                                     >  2:748529/1‑80 (MQ=255)                tCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAg                                                  <  1:748513/81‑1 (MQ=255)                    tACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCgg                                               >  2:748534/1‑80 (MQ=255)                       ggCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCgg                                               >  1:748532/1‑77 (MQ=255)                         ccTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATc                                         <  2:748514/81‑1 (MQ=255)                             tGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGa                                      <  2:748515/80‑1 (MQ=255)                              gTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGAc                                     >  1:748538/1‑80 (MQ=255)                                 gATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCaa                                  <  2:748516/80‑1 (MQ=255)                                      gAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGa                             <  1:748517/80‑1 (MQ=255)                                            ggggCCGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTAtt                      >  2:748536/1‑81 (MQ=255)                                                ccGAGTTTCAATGAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAg                  >  2:748549/1‑81 (MQ=255)                                                            gAATCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAGTCAAAAACggg       >  2:748535/1‑80 (MQ=255)                                                             aaTCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAGTCAAAAACGGGa      <  1:748518/80‑1 (MQ=255)                                                               tCGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAGTCAAAAACGGGaaaa   <  1:748519/81‑1 (MQ=255)                                                                cGCATAAAAATACAAAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAGTCAAAAACGGGAAAAg  >  2:748542/1‑81 (MQ=255)                                                                             |                                                                    AGCATTTCGATAATGTCAGTACGGCCTATGTAGATTTGAAAATGGGGCCGAGTTTCAATGAATCGCATAAAAATAC‑AAAAAAAATGAAGATGTAGCGGCAGATCAGACCAAACTGAAGCTATTTAAGTCAAAAACGGGAAAAG  >  NC_000913/3808334‑3808476

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑