Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,042,775	C→T	R479H (CGC→CAC)	etk ←	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	1,042,775	0	C	T	94.1%	44.8 / ‑5.8	17	R479H (CGC→CAC)	etk	tyrosine‑protein kinase, role in O‑antigen capsule formation
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (7/9);  minor base A (1/0);  total (8/9)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TGCAGACTGGTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACC  >  NC_000913/1042643‑1042890                                                                                                                                     |                                                                                                                    tGCAGACTGGTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTAt                                                                                                               >  2:822779/1‑139 (MQ=255)                         aCGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAg                                                                                       >  1:564144/1‑139 (MQ=255)                                ccACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATa                                                                                >  1:640513/1‑139 (MQ=255)                                                            cGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTgg                                                                                    <  2:223411/107‑1 (MQ=255)                                                            cGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGAGTTTATCCAGCCACTCGGACATTGGGATAGTgg                                                                                    >  1:223411/1‑107 (MQ=255)                                                                                        tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGc                                            >  1:561080/1‑119 (MQ=255)                                                                                        tGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGc                                            <  2:561080/119‑1 (MQ=255)                                                                                             ctgctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa                   <  1:310960/139‑1 (MQ=255)                                                                                             ctgctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa                   <  2:755666/139‑1 (MQ=255)                                                                                             ctgctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCa                   <  1:783539/139‑1 (MQ=255)                                                                                                ctgATTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCAcgc                >  1:679541/1‑139 (MQ=255)                                                                                                   aTTAGAAAATAAATTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGcc             <  1:822779/139‑1 (MQ=255)                                                                                                              aatTTTTCTTACGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCAcc  <  1:423820/139‑1 (MQ=255)                                                                                                                        aCGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTc                                         <  2:268673/90‑1 (MQ=255)                                                                                                                        aCGCAGACGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTc                                         >  1:268673/1‑90 (MQ=255)                                                                                                                              aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc                                                                <  1:625879/61‑1 (MQ=255)                                                                                                                              aCGGGTGTGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGc                                                                >  2:625879/1‑61 (MQ=255)                                                                                                                                     |                                                                                                                    TGCAGACTGGTTCGTAGCGCACGTACGGCTTCCACAGCAGAATCCGCCGGGTTATCCACCGCCAGGAAGGGGATATTTTTAGTACGATGGCGCTGCTGATTAGAAAATAAATTTTTCTTACGCAGACGGGTGCGTTTATCCAGCCACTCGGACATTGGGATAGTGGCATAAACGCTGATGCCGTGCTCTTCCAGTTGTTCCGGGGCTTCTACACCACGACGCAACATCGCACGCGCCAGCACGGCACC  >  NC_000913/1042643‑1042890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑