Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,487,189	G→A	K324K (AAG→AAA)	lptF →	lipopolysaccharide transport system protein LptF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,487,189	0	G	A	90.0%	16.1 / ‑5.9	10	K324K (AAG→AAA)	lptF	lipopolysaccharide transport system protein LptF
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (6/3);  total (6/4)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGGTAAGCTGGACCCGACGCTGTGGATGTGGACCGTTAACCTGATTTATCTGGCTTTAGCGATTGTTCTCAACCTTTGGGACACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTCGCGTAAAGGAGCGGTGTGATGCAACCTTTTGGCGTACTTGACCGCTATATCGGTAAAACTATTTTCACCACCATCATGATGACACTGTTCATGCTGGTGTCGCTGTCGGGCATTATCAAGTTTGTCG  >  NC_000913/4486972‑4487426                                                                                                                                                                                                                          |                                                                                                                                                                                                                                              gcACATTGTGGATCACTGATCCCGATCGTGCTCGCTCAGAACTGAACTGGCGTATCACGTTGGTATTCTCCGTGTTTATGATGTCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCTTACTTTCGATGCTGCCAGCCATGCTGTTGTATCTACTTTCCTTCCTGATCAAGACCTCCCTGAAATCGAACGGCGGTAAAGGTAAACTGGACCCGACGCTGTGGATGTGGACCGTTAAc                                                                                                                                                                                                              <  1:40179/251‑1 (MQ=255)                                                                             tATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGAGGCGGCCAGCCATGCTGCTGTAGCTACTGTTCGTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGTTAAGCTGGACCCGACGCTGTGGATGTGGACCGTTAACCTGATTTATCTgg                                                                                                                                                                                                 <  1:183731/188‑1 (MQ=255)                                                                                   ggCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATAGAACGGCGGTAAAGGAAAACTGGAcc                                                                                                                                                                                                                                        >  1:83513/1‑143 (MQ=255)                                                                                                               gTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGACCGGCGGTCAAGGTAAACTGGACCCGACGCTGGGGATGGGGACCGTTAACCTGATTTCTCTGGCTTTAGCGATTGTTCTCAACCTTTTGGACACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTTGCGTAAAGGGGCGGGGTGATGCAACCTTTTggg                                                                                                >  1:143008/1‑250 (MQ=255)                                                                                                                 tAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGCATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGGTAAACTGGACCCGAAGCTGGGGGTGTGGACCGTTAACCTGATTTATCTGGCTTTAGCGATTGTTTTCCACCTTTGGGACACACTGCCGGTCCGCCGCCTgcgc                                                                                                                                            >  1:146542/1‑205 (MQ=255)                                                                                                                  aaCCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGGTAAACTGGACCCGACGCTGTGGATGTGGACCGTTAACCTGATTTATCTGGCTTTAGCGATTGTTCTCAACCTTTGGGACACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTCGCGTAAAGGAGCGGTGTGATGCAACCTTTTGGCGt                                                                                              <  1:16693/250‑1 (MQ=255)                                                                                                                                                  gccagccaTGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCGGAAATCGAACGGCGGTAAAGGTAAACTGGACCCGACGCTGTGGATGTGGACCGTTAACCTGATTTATCTGGCTTTAGCGATTGTTCTCAACCTTTGGGac                                                                                                                                                                    <  1:91/148‑1 (MQ=255)                                                                                                                                                                   aTCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGGCAAACTGGACCCGCCGCTGCGGATGTGGAACGTTAACCTGCTTTATCTGGCTTTAGCGATTGTTCTCAACCTTTGGGACACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTCGCGTAAAGGAGCGGTGTGATGCAACCTTTTGGCGTACTTGACCGCTATATCGGTAAAACTATTTTCACCACCATTATGATGacac                                            >  1:139453/1‑251 (MQ=255)                                                                                                                                                                       aCTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGGTAAACTGGACCAGCCGCCGTGCATGTGGACCGTTCAACTGAATTGTCTGGCTTTAGCGATTGCTCTCAAACTTTGGGGAACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTCGCGCAAAGGAGCGGAGTGATGCCACCTTTTTGCGTACTTGACCACTATATCGGGAAAACTATTTTCACCCCCATCCTAATGACACTGtt                                        >  1:227836/1‑251 (MQ=255)                                                                                                                                                                                                              cggTAAAGGTAAACTGGACCCGACACTGTGGATGTGGACCGTTAACCTGATTTATCTGGCTTTAGCGATTGTTCTCAACCTTTGGGACACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTCGCGTAAAGGAGCGGTGTGATGCAACCTTTTGGCGTACTTGACCGCTATATCGGTAAAACTATTTTCACCACCATCATGATGACACTGTTCATGCTGGTGTCGCTGTCGGGCATTATCAAGTTTGTCg  >  1:206743/1‑250 (MQ=255)                                                                                                                                                                                                                          |                                                                                                                                                                                                                                              GCACATTGTGGAACACTGACACCGATCGTGCTCGCGCAGAACTGAACTGGCGTATCACGTTGGTATTCACCGTGTTTATGATGGCACTTATGGTCGTACCGCTGAGCGTGGTTAACCCACGTCAGGGACGCGTACTGTCGATGCTGCCAGCCATGCTGCTGTATCTACTTTTCTTCCTGATCCAGACCTCCCTGAAATCGAACGGCGGTAAAGGTAAGCTGGACCCGACGCTGTGGATGTGGACCGTTAACCTGATTTATCTGGCTTTAGCGATTGTTCTCAACCTTTGGGACACCGTGCCGGTCCGCCGCCTGCGCGCCAGTTTTTCGCGTAAAGGAGCGGTGTGATGCAACCTTTTGGCGTACTTGACCGCTATATCGGTAAAACTATTTTCACCACCATCATGATGACACTGTTCATGCTGGTGTCGCTGTCGGGCATTATCAAGTTTGTCG  >  NC_000913/4486972‑4487426

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑