Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	657,282	G→A	intergenic (+165/‑10)	pagP → / → cspE	Lipid A palmitoyltransferase/transcription antiterminator and regulator of RNA stability CspE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	657,282	0	G	A	96.2%	89.6 / NA	26	intergenic (+165/‑10)	pagP/cspE	Lipid A palmitoyltransferase/transcription antiterminator and regulator of RNA stability CspE
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (11/14);  minor base C (1/0);  total (12/14)
Fisher's exact test for biased strand distribution p-value = 4.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGATGACCTACATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGTAATCGCTCTGTAAGATACGTCAGCAAGAATTCAA  >  NC_000913/657047‑657522                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                 aGATGACCTACATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCt                                                                                                                                                                                                                                   <  1:392353/251‑1 (MQ=255)      aCCTACATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGTACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATGTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGag                                                                                                                                                                                                                              <  2:339132/251‑2 (MQ=255)       ccTACATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGAtt                                                                                                                                                                                                                             <  1:382365/251‑1 (MQ=255)          aCATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTaaa                                                                                                                                                                                                                          <  1:89078/251‑1 (MQ=255)          aCATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTGTCAGTTTTGAGACAAATGAAGTTTTAGTAACGTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAAGAACGCGTCTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGGGTACTGGTAACCGACACAGCAATTGTGTCTATTGTTCATGTAAAAGTAATTTTGATGTCGAAGATTaaa                                                                                                                                                                                                                          <  2:308329/251‑1 (MQ=255)           cATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTaa                                                                                                                                                                                                                           >  1:142317/1‑249 (MQ=255)            aTTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAgg                                                                                                                                                                                                                        >  2:473702/1‑251 (MQ=255)                cGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGTCTTTTATCTCTTTTTAGTAAAGTTACACTGGACAAATCGTACCACAATTGTTGTACTTGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAAc                                                                                                                                                                                                                    <  2:498241/251‑1 (MQ=255)                     aCCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTa                                                                                                                                                                                                                >  1:265249/1‑250 (MQ=255)                                                 ccTGGAAGCGCTTTCAGTTTTGAGACACCTGAAGTTTTAGTAACTTCTTTAAAATCACTAGCTAAAATAAGTAACATCACAAATAAAGCGCCTTTTATCACTCTTTAGTAAAGTTACACTGGACAAAGCGTACCCCAATTGGAGCACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTATAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGt                                                                                                                                                                                   >  2:204142/1‑251 (MQ=255)                                                                    ttGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGAc                                                                                                                                                                 <  1:373921/250‑1 (MQ=255)                                                                     tGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACg                                                                                                                                                                <  2:251875/250‑1 (MQ=255)                                                                      gagaCAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGgc                                                                                                                                                              <  1:128895/251‑1 (MQ=255)                                                                         aCAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGgcagc                                                                                                                                                           >  2:366671/1‑251 (MQ=255)                                                                           aaaTGAAGTTTTAGTAACTTCTTTAAAATCAATATCTAAAATAAGTAACATCAAAAATACCGCTACTTTTATCTCTTTTTAGTAAAGTTACACTTGACTATGCGTACCACAATTGGTGTACTGGTAACCGACACAGCAGTTGTGGCTATTTTTCATGTAAAAGTATTTATGATGTCTAATATTAAAGGGATCGTTAAGTGGTTTAATGAGTCCAAAGGATTCTGTTGCATTACTCCGGAAGACGGCAGCaa                                                                                                                                                         <  2:286176/251‑1 (MQ=255)                                                                                              tcttTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACt                                                                                                                                        <  1:366671/249‑1 (MQ=255)                                                                                                    aaaacAATAACTAAAATAAATAACAACAAAAATAACGCGACTTTTTTCACGTTTTAGTAAATGTACACGGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCa                                                                                                                                <  2:331663/247‑1 (MQ=255)                                                                                                                 aaaTAACTACCATCCAACATAACGCGACTTTTATCACTGTTTAGTACAGTTACACTGGACAAAGCGTACCAAACTTGGGGTCCTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAACGGACTTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTATTCGGGAAGACGGAAGCAAAGACGTGTTCGTCCCCTTCTCTGCAATCACGACTAATg                                                                                                                   >  2:221572/1‑251 (MQ=255)                                                                                                                            aTCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACCGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAAct                                                                                                        >  2:361971/1‑251 (MQ=255)                                                                                                                                     aaCGCGACGTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACCATTGGTGTACTGGTAACCGAAACAACATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAAACGGCAGCAAAGACGTGATAGTACACTTCTCTGCACTCCAGACTCATGGTTTTAAAACTCTTGCTGa                                                                                                >  2:276518/1‑250 (MQ=255)                                                                                                                                                                aGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACt                                                                    >  1:132613/1‑251 (MQ=255)                                                                                                                                                                                             ggTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCaa                                        >  1:322178/1‑250 (MQ=255)                                                                                                                                                                                                gtACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAACAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGt                                    >  1:264342/1‑251 (MQ=255)                                                                                                                                                                                                              cacaGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGTAATCGCTCTGTAAg                      <  2:265249/251‑1 (MQ=255)                                                                                                                                                                                                                caGCATTTGTGTCTATTTTTCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGTAATCGCTCTGTAAGAt                    <  2:132613/251‑1 (MQ=255)                                                                                                                                                                                                                                   tCATGTAAAAGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGCGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGTAATCGCTCTGTAAGATACGTCAGCAAGAATTCaa  >  1:465325/1‑250 (MQ=255)                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                 AGATGACCTACATTCCGGGTACCTACAACAATGGCAATGTGTACTTTGCCTGGATGCGCTTTCAGTTTTGAGACAAATGAAGTTTTAGTAACTTCTTTAAAATCAATAGCTAAAATAAGTAACATCAAAAATAACGCGACTTTTATCACTTTTTAGTAAAGTTACACTGGACAAAGCGTACCACAATTGGTGTACTGGTAACCGACACAGCATTTGTGTCTATTTTTCATGTAAAGGTAATTTTGATGTCTAAGATTAAAGGTAACGTTAAGTGGTTTAATGAGTCCAAAGGATTCGGTTTCATTACTCCGGAAGACGGCAGCAAAGACGTGTTCGTACACTTCTCTGCAATCCAGACTAATGGTTTTAAAACTCTTGCTGAAGGTCAGCGCGTAGAGTTCGAAATCACTAACGGTGCCAAAGGCCCTTCTGCTGCAAACGTAATCGCTCTGTAAGATACGTCAGCAAGAATTCAA  >  NC_000913/657047‑657522

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑