Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,643,679	A→T	L209Q (CTG→CAG)	ydfU ←	protein YdfU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,643,679	0	A	T	95.5%	61.9 / ‑3.8	22	L209Q (CTG→CAG)	ydfU	protein YdfU
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base T (11/10);  total (12/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.56e-01

GTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGATTCC  >  NC_000913/1643487‑1643915                                                                                                                                                                                                  |                                                                                                                                                                                                                                             ttCTTAACCTTACGTGTGTATTTTTCCTTAATCCAGTGGCGACGTGTAGGCAGCTTCATGAAATATTTCTGAGACTCTGGTTCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGTGCGTAAGGCATCGGTGCAAGATTTTTTGTGCGTTGTTTTAATATGCTG‑GTGGCGGTCTGCTTTCCCGGTACGATGTCGCTTTCGCGGTTCACCGAGCAGATTTTTTCCGCTGGTa                                                                                                                                                                                     <  2:329237/249‑1 (MQ=255)                               aCCCAGCGGCGACGTTTAGGCAGCTTCATGAACGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTACTGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCCGATTTTTTCCGCTGGTGATCCCAACGCACGCCGCGATACAACCACAgg                                                                                                                                                      >  2:112481/1‑251 (MQ=255)                                  cAGCGGCGACGTTTAGGCAGCTTCATGCAAGATTCAGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GAGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGATGGTACTCCCAGAGAAAGACGCGATACCGCCCCAGGt                                                                                                                                                     >  2:352387/1‑249 (MQ=255)                                                           tGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGt                                                                                                                                                     >  1:35657/1‑224 (MQ=255)                                                              aaGAGTCCTGAGACTCTGGATCAACGGTGATGCTTTCCACCGTCGTTGCCTGTGGTGATTGTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTCGTTTCAATATGCTG‑TTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACAACGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGTTAGTGCATCCACCACCTGATTGCAGACCGcc                                                                                                                       <  1:387/251‑1 (MQ=255)                                                                        agaCTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGAt                                                                                                              >  1:343565/1‑250 (MQ=255)                                                                             ctGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTc                                                                                                         >  1:128575/1‑250 (MQ=255)                                                                               ggatcatgtttGATTCTTATCACCGTCTTTTCCTGTTGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGAAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGTGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAACCCCATCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGTCCACCAGGATAATTc                                                                                                         <  2:92537/238‑1 (MQ=255)                                                                               ggATCAACGGTGATGCTTTCCACCGTCTTTTCCTGTGGTTATTTTTGTTGCTGGTGGGCGTAAGGCACTGGTGCACGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTTCGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGTTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCCCCTGATTGCAGACCGCCCACCAGGATAATTCa                                                                                                        <  1:137977/249‑1 (MQ=255)                                                                               ggATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAg                                                                                                       <  1:129550/250‑1 (MQ=255)                                                                                            tGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGACTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTcc                                                                                         >  1:35937/1‑251 (MQ=255)                                                                                                   caccGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGAAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAACGATAATTCCCGCTCCt                                                                                  >  1:345560/1‑251 (MQ=255)                                                                                                      cGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCg                                                                               >  1:185294/1‑251 (MQ=255)                                                                                                       tgttttgccTGTGGTGATTTGTTTTGCGGGTGGGCGGAAGGCAACTGTTCAAGATCTTGTGTGCTTTGTTTCAATTTG‑TGTGTGGCGTTCTTCTCTCCCGGTCCTATGTCGCTTTTGCGGCACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCTAACGCCGCGATTCAGCCTCATTGAGTGCATCCACCACCCGATTGCAGACCTCGCACCAGGTTAATTCAGCCAACGATAAGTCCCGCTCCTGCg                                                                               <  2:367096/243‑1 (MQ=255)                                                                                                            ttCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACAACGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACa                                                                                                                                                              >  1:165656/1‑166 (MQ=255)                                                                                                            ttCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGGTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGGACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACa                                                                                                                                                              <  2:165656/166‑1 (MQ=255)                                                                                                                                       ggCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACCCCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCa                                              <  1:328777/251‑1 (MQ=255)                                                                                                                                                 aaCGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACCATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGCTTCCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCCCTCCTCCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCctgctgc                                    >  1:332190/1‑250 (MQ=255)                                                                                                                                                          aGATTTTTTGGTCTTTGTTGCAATATTCTG‑GTGGCGGTCTGCTCTCCAGGTACGATTTCGCTTTCTCGGTACACCGAGCAGATTTTGTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCCTCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTttg                           <  2:35937/251‑1 (MQ=255)                                                                                                                                                           gATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTttgt                          >  1:118163/1‑251 (MQ=255)                                                                                                                                                                   gtgagttgttTCAATATGCTG‑GAGGCGGTCAGCTCTCCCGGGACGATATCGCTTTAGCGGTACACCGAGCAGATATTTTCCGCTGGTAATCCCAGCGAACGACGCGATACGGCCTCAGGGAGTGCATCCACCACCTGCTTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACAGCTTATTGCGTGACGGATGAAGGAAATCACGCATGCTGTCCGCATTTGTTGagca                    >  2:99496/5‑249 (MQ=255)                                                                                                                                                                                    gCTG‑GTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGATTcc  <  1:112481/250‑1 (MQ=255)                                                                                                                                                                                                  |                                                                                                                                                                                                                                             GTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTG‑GTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGATTCC  >  NC_000913/1643487‑1643915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑