Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,041,940	C→A	30.0%	intergenic (+25/+90)	appA → / ← etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,041,940	0	C	A	30.0%	30.3 / 15.3	20	intergenic (+25/+90)	appA/etk	phosphoanhydride phosphorylase/tyrosine‑protein kinase, role in O‑antigen capsule formation
Reads supporting (aligned to +/- strand):  ref base C (7/7);  new base A (3/3);  total (10/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

GCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCC  >  NC_000913/1041820‑1042019                                                                                                                         |                                                                                gCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTg                                                                     <  1:849631/133‑1 (MQ=255) gCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTg                                                                     >  2:849631/1‑133 (MQ=255)             gagCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGGTAACTGaa                                                                            >  4:196120/1‑114 (MQ=255)             gagCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGGTAACTGaa                                                                            <  3:196120/114‑1 (MQ=255)                 gAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGaa                                                                            >  4:574761/1‑110 (MQ=255)                 gAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGaa                                                                            <  3:574761/110‑1 (MQ=255)                         cAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGGTAACTGAATGc                                                                         <  1:255761/105‑1 (MQ=255)                         cAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGGTAACTGAATGc                                                                         >  2:255761/1‑105 (MQ=255)                                     tCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCg                                    <  4:1131290/130‑1 (MQ=255)                                     tCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCg                                    >  3:1131290/1‑130 (MQ=255)                                                     cGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTAc                                                                                 <  4:903261/69‑1 (MQ=255)                                                     cGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTAc                                                                                 >  3:903261/1‑69 (MQ=255)                                                                aatgaaGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAAc                                               >  4:495264/1‑92 (MQ=255)                                                                aatgaaGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAAc                                               <  3:495264/92‑1 (MQ=255)                                                                       cACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTg                                             <  2:665142/87‑1 (MQ=255)                                                                       cACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTg                                             >  1:665142/1‑87 (MQ=255)                                                                                           ttGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACaa                                                        <  3:170367/56‑1 (MQ=255)                                                                                           ttGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACaa                                                        >  4:170367/1‑56 (MQ=255)                                                                                                              gCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGcc  <  1:256001/91‑1 (MQ=255)                                                                                                              gCATTCAGGTAACTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGcc  >  2:256001/1‑91 (MQ=255)                                                                                                                 ttCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGt                                            >  4:333936/1‑46 (MQ=255)                                                                                                                 ttCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGt                                            <  3:333936/46‑1 (MQ=255)                                                                                                                         |                                                                                GCAGGATGTGAAGAGCGAAATGCGCAGGGCATGTGTTCGTTGGCAGGTTTTACGCAAATCGTGAATGAAGCACGCATACCGGCGTGCAGTTTGTAATGCATAAAAAAGAGCATTCAGTTACCTGAATGCTCTGAGGCTGATGACAAACGAAGAACTGTCTAATGCGTAGACCGGAAAAGGCGTTCACGCCGCATCCGGCC  >  NC_000913/1041820‑1042019

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑