Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,268,985	G→A	Q44Q (CAG→CAA)	lpxT →	lipid A‑core phosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,268,985	0	G	A	95.5%	61.8 / ‑3.0	22	coding (132/714 nt)	lpxT	lipid A‑core phosphotransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (13/8);  minor base . (1/0);  total (14/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

CGAAGCTGACTGGAATGCCTTGCAGAGCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAGAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTAAACCAGCTGGGTCAGGCATTAATTCCTGTAAAACGGGCCAGCCCAACATTGACTTTTACCG  >  NC_000913/2268752‑2269229                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                      cGAAGCTGACTGGAATGCCTTGCAGAGCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTa                                                                                                                                                                                                                                      >  2:128146/1‑250 (MQ=255)  gAAGCTGACTGGAATGCCTTGCAGAGCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAGAGTAAg                                                                                                                                                                                                                                    <  1:99636/251‑1 (MQ=255)  gAAGCTGACTGGAATGCCTTGCAGAGCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAg                                                                                                                                                                                                                                    <  2:305649/251‑1 (MQ=255)                 gCCTGGCAGAGCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAAGATGATTAAAAATTTGCCTCAAAGAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTTCCGATTGATGCTGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTg                                                                                                                                                                                                                     <  2:352404/251‑1 (MQ=255)                         gagCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCAtt                                                                                                                                                                                                             >  1:299956/1‑251 (MQ=255)                                                                  gTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCgg                                                                                                                                                                    >  1:353454/1‑250 (MQ=255)                                                                                    tAAGATACTTAGAAACAATCTGATTAAAAATTTCCCGCAAATCGTGTTGTTGAATATTAACGGCCTGACGATGATTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATCTTTTTTATTTCTTTAATCAAACAC‑TGGACGAAAGTAAGACCTTTTTGTGGCCGGTTGCATAGACCACCAATCGAGCCTTAGAAGGTTTTTAACTGACGGAGATGGGTATGTTGATCCTgc                                                                                                                                                  >  2:336016/1‑250 (MQ=255)                                                                                    tAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTg                                                                                                                                                   >  1:260322/1‑250 (MQ=255)                                                                                              agagAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGAGGCTGAGTTTCTGGCt                                                                                                                                        <  1:75064/251‑1 (MQ=255)                                                                                                                aaTTTGCCGAATATAGTGTTGATGAATATTGTCTTCATAGCGCTTTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGTTTGCCGATTGATGCGGACATTTTTAATATCTTTATTCA‑AAACACGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTGGCATTTACCACAAATAGCGCCTTCGACAGTTGTTTACTGCTGACGGTGGAGATGATGATTCTGGGTTTCTGGCTGGAAGAATACgaccatgg                                                                                                                      >  2:263209/1‑244 (MQ=255)                                                                                                                          aaaTAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGt                                                                                                            >  2:255690/1‑251 (MQ=255)                                                                                                                                  ttgttgAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTTTTCACTGCTGGCGATGGGGATGATGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGAAGACGTGTCGTgct                                                                                                    >  2:241412/1‑249 (MQ=255)                                                                                                                                         atatTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGTTTGTTGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTGTGTTGATGCTGAGTTTCTGGGTGAAAGAAAACGCCCCTGGCAGAAGACGTATCGTGATTATtggt                                                                                             >  1:193441/1‑251 (MQ=255)                                                                                                                                         atatTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATtggt                                                                                             >  2:248501/1‑251 (MQ=255)                                                                                                                                                    cTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGGATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCt                                                                                  >  2:79813/1‑251 (MQ=255)                                                                                                                                                                     cTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATAGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAACGAAAACGCCCCTGGCCGCCGGCGTATCGTGATTATTGGTCTGGTCCTGCTATTAACTGCAGTGGTAt                                                                 >  2:226946/1‑251 (MQ=255)                                                                                                                                                                     cTGGTATATACCCGTTAATCATGGCTTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAAAAATCGCGCCTTCGACGGTTGTTCCCTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGACAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCCTGCTATTAACTGCAGTGGTAt                                                                 >  2:167960/1‑251 (MQ=255)                                                                                                                                                                       ggTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTa                                                               <  1:290467/251‑1 (MQ=255)                                                                                                                                                                              ccccGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTAAACCAg                                                         <  1:57285/250‑1 (MQ=255)                                                                                                                                                                                                                gCGGATATTTTTTATTTCTTTAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTAAACCAGCTGGGTCAGGCATTAATTCCTGTAAAACGGGCCa                       <  1:79813/250‑1 (MQ=255)                                                                                                                                                                                                                                   ttAATCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTAAACCAGCTGGGTCAGGCATTAATTCCTGTAAAACGGGCCAGCCCAACATTGACTTTTAcc   >  1:45420/1‑251 (MQ=255)                                                                                                                                                                                                                                     aaTCAAAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTAAACCAGCTGGGTCAGGCATTAATGCCTGTAAAACGGGCCAGCCCAACATTGACTTTTACCg  <  1:324994/250‑1 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                                                      CGAAGCTGACTGGAATGCCTTGCAGAGCGCGCTGTTGAAGCTTCGTTTAGCGACTACCGCGTAAGGTTGCCTGCGTTTTTCAGTAAGATAATTAGAGAAAATATGATTAAAAATTTGCCGCAAATAGTGTTGTTGAATATTGTCGGCCTCGCGCTGTTTCTTTCCTGGTATATCCCCGTTAATCATGGATTCTGGTTGCCGATTGATGCGGATATTTTTTATTTCTTTAATCAGAAAC‑TGGTCGAAAGTAAGGCCTTTTTGTGGCTGGTTGCATTGACCAACAATCGCGCCTTCGACGGTTGTTCACTGCTGGCGATGGGTATGTTGATGCTGAGTTTCTGGCTGAAAGAAAACGCCCCTGGCAGACGACGTATCGTGATTATTGGTCTGGTCATGCTATTAACTGCAGTGGTATTAAACCAGCTGGGTCAGGCATTAATTCCTGTAAAACGGGCCAGCCCAACATTGACTTTTACCG  >  NC_000913/2268752‑2269229

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑