Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,797,329	C→T	L128L (CTA→TTA)	waaL →	O‑antigen ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,797,329	0	C	T	100.0%	69.4 / NA	22	L128L (CTA→TTA)	waaL	O‑antigen ligase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (8/14);  total (8/14)

TATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGCTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAAATAGTTGCGCGGTACTTTATGT  >  NC_000913/3797111‑3797570                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                  tATTGTCACTAATTTTACGAGGCCGAAAAGAAAATTATAATATAAAAAACATTTTTCTTCCCCTTTATATATTTTTCATAGGCTTGCTTGACTTAATTTGGTATTCTGCTTTTACAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTTACACAATATTTATATTTGGTTCTTTTATTGTTTTCTTTAACCTCACTAGCCAGTTAAAATCAAAAAGAGAGTGTGTATTTTACACt                                                                                                                                                                                                                   >  2:166043/1‑251 (MQ=255)       cACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAGAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTAt                                                                                                                                                                                                             >  1:71501/1‑251 (MQ=255)           aaTTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATtc                                                                                                                                                                                                           <  1:309462/249‑1 (MQ=255)                     ggCAGACAAGAAAATTATAATATAAAAAACCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCt                                                                                                                                                                                               <  1:118921/251‑1 (MQ=255)                                             aaaaaCCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACtt                                                                                                                                                                                                                  >  1:170912/1‑208 (MQ=255)                                             aaaaaCCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACtt                                                                                                                                                                                                                  <  2:170912/208‑1 (MQ=255)                                                     tATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATGCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACGGCCAAAATATTTATATTTGGTTCTTTTATTGTTGTCTTGGCACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTGTTTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGc                                                                                                                                                                <  1:200516/250‑1 (MQ=255)                                                      aTTCATCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTAGTCTGCGTTTAAAGTAGATAATTCGACATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTTACCAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCAt                                                                                                                                                              <  1:197123/251‑1 (MQ=255)                                                                     atatTTTTAATAGGCATGCTTGATTTAATTTGGTATTCTGCGAATACAGTAGATAATTCGACATTTCATGCTACTTACAATAGTTATTTAACTACTGCCAAAATATTTTTATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCACAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGACATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCg                                                                                                                                               >  1:394395/1‑251 (MQ=255)                                                                       atTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCa                                                                                                                                             <  1:210868/251‑1 (MQ=255)                                                                                aGGCTTGCTTCATTTATTTTGGAATTCTGCGTTTAAAGGAGATAATTCGCCATTTCGTGCTACTTACCATAGTTCTATAAATCCTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTCGCACGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTATTAGCATTAATGAAAATGACAGCATTTCTTTTg                                                                                                                                    >  2:437372/1‑251 (MQ=255)                                                                                                                                                            ttAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTtata                                                         <  1:133234/250‑1 (MQ=255)                                                                                                                                                                  aCTGCCAAAATATTTATAGTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGa                                                   <  2:247290/250‑1 (MQ=255)                                                                                                                                                                                       ggTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTtttttattttt                             <  1:124191/251‑1 (MQ=255)                                                                                                                                                                                              ttATTGTTTTCTTGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTaaa                       <  1:226852/250‑1 (MQ=255)                                                                                                                                                                                                      ttCTTGTCACTAACTAGCCAGTTAAAATCAAAACAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTTATAGCATTCATGAACATGCTCGCATTTCTTTTGGTGTAGTATCGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGTATATTTATTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTGTGAGTTTTAGTAAATAGTTgcg               <  2:71501/250‑1 (MQ=255)                                                                                                                                                                                                         ttGACACTAACTAGCCAGTTAAAATCAAACAAAGAGAGCGTATTATCCACTTTGCAATCTCTGTCATTACTAATTGCTGGCTATGCAAAGTATATTAATAGAATTCATGAAAATGAACGCATTTCTTTTGGTGAATGAACGGCAACAGGAGCCGCATCTTCACCAATGCTATTCGGGATAGTTAGTGGCATAGCAATTCTTTATACTAAGAAAAATAATCCTTTTTTATTTTTATTAAATAGTTGCGCGGt           >  2:201551/1‑251 (MQ=255)                                                                                                                                                                                                          tGACACTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAAATAGTTGCGCgg            <  1:78280/249‑1 (MQ=255)                                                                                                                                                                                                            acacTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAAATAGTTGCGCGGTACt        >  1:283157/1‑251 (MQ=255)                                                                                                                                                                                                             cacTAACTAGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTTGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGATCAGCATATGCAACAATGCTGATAGGGATAGTTATTGTTGTTGCGATTCTGTATACGGAGAAAAAGCATTCTGTTTTATTTTTAGTAAATAGGTGCGGGGTACtt       <  2:49029/251‑1 (MQ=255)                                                                                                                                                                                                              actaactaGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTATTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAAATAGTTGCGCGGTACttt      >  2:123345/1‑251 (MQ=255)                                                                                                                                                                                                                  actaGCCAGTTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAAATAGTTGCGCGGTACTTTATGt  <  1:251681/251‑1 (MQ=255)                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                  TATTGTCACTAATTTTACGTGGCAGACAAGAAAATTATAATATAAAAAACCTTATTCTTCCCCTTTCTATATTTTTAATAGGCTTGCTTGATTTAATTTGGTATTCTGCGTTTAAAGTAGATAATTCGCCATTTCGTGCTACTTACCATAGTTATTTAAATACTGCCAAAATATTTATATTTGGTTCTTTTATTGTTTTCTTGACACTAACTAGCCAGCTAAAATCAAAAAAAGAGAGTGTATTATACACTTTGTATTCTCTGTCATTTCTAATTGCTGGATATGCAATGTATATTAATAGCATTCATGAAAATGACCGCATTTCTTTTGGTGTAGGAACGGCAACAGGAGCAGCATATTCAACAATGCTAATAGGGATAGTTAGTGGCGTTGCGATTCTTTATACTAAGAAAAATCATCCTTTTTTATTTTTATTAAATAGTTGCGCGGTACTTTATGT  >  NC_000913/3797111‑3797570

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑