Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,109,742	C→T	L64L (CTA→TTA)	yqgA →	DUF554 domain‑containing protein YqgA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,109,742	0	C	T	88.9%	15.9 / ‑3.2	9	L64L (CTA→TTA)	yqgA	DUF554 domain‑containing protein YqgA
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (2/6);  total (2/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01

ACCAAACGGTCATAATAAGAAAATCAAACAATACAGCTAACAGGAACTCTTGTGGTCATCGGCCCTTTTATCAACGCTAGTGCAGTCTTACTGGGTGGCGTTCTCGGCGCACTGCTCAGCCAACGCTTACCGGAACGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGCTACTTGGCGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGGTGTCAATACAGCAGTCGCCAAAGCACAAAATCTGTTTCGTCACTCACGTAAGAAGCCAGCGCATGAATCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTCTTGATTTCTTTAC  >  NC_000913/3109502‑3109986                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                     aCCAAACGGTCATAATAAGAAAATCAAACAATACAGCTAACAGGAACTCTTGTGGTCATCGGCCCTTTTATCAACGCTAGTGCAGTCTTACTGGGTGGCGGTCTCGGCGCATGGCTCAGCCAGCTCTTACCGGAACGTATCCGCGTCTCCATGACAGCTATTTTTGGTCTGGCATCGCTGTGGGTTGGTATTGTACTGTTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTGAGCTACGTTACTTGgcgc                                                                                                                                                                                                                                            <  1:34492/251‑1 (MQ=255)           cATAATAAGAAAATCAAACAATACAGCTAACAGGAACTCTTGTGGTCATCGGCCCTTTTATCAACGCTAGTGCAGTCTTACTGGGTGGCGTTCTCGGCGCACTGCTCAGCCAACGCTTACCGGAACGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGTTACTTGGCGCTCTAATTggn                                                                                                                                                                                                                                  <  1:52379/251‑2 (MQ=255)                     aaaTCAAACAATACAGCTAACATGAACTCTTGTGGTCATCGGCCCTTTTATCAACGCTAGTGCAGTCTTACTGGGTGGCGTTCTCGGCGCACTGCTCAGCCAACGCTTACCGGAACGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGTTACTTGGCGCTCTAATTGGCGAAAtttgtn                                                                                                                                                                                                                        <  1:56060/251‑2 (MQ=255)                     aaaTCAAACAATACAGCTAACAGGAACTCTTGTGGTCATCGGCCCTTTTATCAACGCTAGTGCAGTCTTACTGGGTGGCGTTCTCGGCGCACTGCTCAGCCAACGCTTACCGGAACGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGCTACTTGGCGCTCTAATTGTCGAAAtttgtt                                                                                                                                                                                                                        <  1:66294/251‑1 (MQ=255)                                                                                                   ngTTCTCGGCGCACTGCTCAGCCAACGCTTACCGGAACGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGTTACTTGGCGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGGTGTCAATACAGCAGTCGCCAAAGCACAAAATCTGTTTCGTCACTCACGTAAGAAGCCAGCGCATg                                                                                                                                          >  1:44401/2‑251 (MQ=255)                                                                                                                                       aCGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATGTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGTTACTTGGCGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGGTGTCAATACAGCAGTCGCCAAAGCACAAAATCTGTTTCGTCACTCACGTAAGAAGCCAGCGCATGAATCTTTTATTCAGAATTATGTCGCGATTATTGTcn                                                                                                      <  1:19083/251‑2 (MQ=255)                                                                                                                                              cgcgGCTCCATTACATCAATTTTTGGTCTGGCATCTCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGAGATGGTTTTAGCTACGTTACTTCGCGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGgtgt                                                                                                                                                                                                        <  1:200178/146‑1 (MQ=255)                                                                                                                                                                                                                                     gTTTTNGCTACNTNNCTTGGTGCTCTAATTGGCGNAATTTGTTTGCTGGANAAAGNTGTCANTan                                                                                                                                                                                                  >  2:81604/1‑64 (MQ=255)                                                                                                                                                                                                                                     gTTTTAGCTACGTTACTTGGTGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGGTGTCAATACAGCAGTCGCCAAAGCACAAAATCTGTTTCGTCACTCACGTAAGAAGCCAGCGCATGAATCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAgg                                                        <  1:81604/203‑1 (MQ=255)                                                                                                                                                                                                                                           gctacgttacTTGGCGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGGTGTCAATACAGCAGTAGCCAAAGCACAAAATCTGTTTCGTCACTCACGTAAGAAGCCAGCGCATGAATCTTTTATTCAGAATTATGTCGCGATTATTGCCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTCTTGATTTCTTTAc  >  1:213025/1‑251 (MQ=255)                                                                                                                                                                                                                                                 |                                                                                                                                                                                                                                                     ACCAAACGGTCATAATAAGAAAATCAAACAATACAGCTAACAGGAACTCTTGTGGTCATCGGCCCTTTTATCAACGCTAGTGCAGTCTTACTGGGTGGCGTTCTCGGCGCACTGCTCAGCCAACGCTTACCGGAACGTATCCGCGTCTCCATGACATCAATTTTTGGTCTGGCATCGCTGGGGATTGGTATTTTACTGGTGGTGAAATGTGCCAACCTTCCAGCGATGGTTTTAGCTACGCTACTTGGCGCTCTAATTGGCGAAATTTGTTTGCTGGAGAAAGGTGTCAATACAGCAGTCGCCAAAGCACAAAATCTGTTTCGTCACTCACGTAAGAAGCCAGCGCATGAATCTTTTATTCAGAATTATGTCGCGATTATTGTCCTGTTTTGCGCCAGCGGCACCGGGATCTTCGGGGCGATGAACGAAGGGATGACCGGCGATCCGAGTATTTTAATCGCCAAGTCATTTCTTGATTTCTTTAC  >  NC_000913/3109502‑3109986

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑