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	89.5%	44.0 / ‑0.8	19	L209Q (CTG→CAG)	ydfU	protein YdfU
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base T (4/13);  total (5/14)
Fisher's exact test for biased strand distribution p-value = 4.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.34e-01

AATCAGATGATGCGGATCGTCGGCTGGCATACCGCAGCAAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGATTCCGA  >  NC_000913/1643435‑1643917                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                               aaTCAGATGATGCGGATCGTCGGCTGGCATACCGCAGCAAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCtctc                                                                                                                                                                                                                                          <  1:102517/251‑1 (MQ=255)      gatgatGCGGATCGTCGGCTGGCATACCGCAGCAAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGt                                                                                                                                                                                                                                     <  2:264275/251‑1 (MQ=255)                          ggCATACCGCAGCAAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTa                                                                                                                                                                                                                 <  1:195838/251‑1 (MQ=255)                           gcctACCGCAGCAAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGAGCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTac                                                                                                                                                                                                                <  1:219834/248‑1 (MQ=255)                                   cagcaAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCa                                                                                                                                                                                                        <  1:10165/251‑1 (MQ=255)                                                gCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGCTTTTTGTTGCTGGTGGGCGTAAGGCAACGGAGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCAGCTCTCACGGTACGATGTCGCTTTCGCGTTACACCGAGCAGTTTTTTTCCGCt                                                                                                                                                                                           >  2:116221/1‑251 (MQ=255)                                                   gtttCTTAACACAACTTGTGTATGTCTCCTTAACCCAGCGGCGACTTTTAGGCTGCTTCATGAAAGATTCCGGAGACTCTGGATCTACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTGTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGTTACACCGTGCAGATTTTTTCCGCTg                                                                                                                                                                                          <  2:37658/246‑1 (MQ=255)                                                     gtCTTAACCCAACGTGTGTATTTATCCTTAACCCAGCGGCGACGTAAAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTCCCACCGTCTTTGCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATTCTGGTGGCGGTCTGCTCTCCCGGGACGTTGTCGAGTTCGCGGAACACCGAACACGTTTTTTCAGATGGTa                                                                                                                                                                                       >  2:84056/1‑250 (MQ=255)                                                                                       aGCGGCTACGTTTAGGCATCTTCATGAAAGATTCCGGAGACTCTTGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGt                                                                                                                                                    <  1:28014/251‑1 (MQ=255)                                                                                               cGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATccac                                                                                                                                            <  1:186814/251‑1 (MQ=255)                                                                                                                            ggaCTCTGGATCAACGGTTATGCTTACCACCGTCTTTTCCTGGTATGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGGGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATa                                                                                                               <  2:225319/250‑1 (MQ=255)                                                                                                                                                   ttACCACCGTCTTTTCCTGTGTTGATTTTTGTTGCTGGTGGGCGGAAGGCAGCGGTGCAAGATTTTTTGTGCGTGGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCg                                                                                         <  1:147197/250‑1 (MQ=255)                                                                                                                                                               tttCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGTAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTATGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAAAGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGACCACCAGGATAATTTAGCCAAAGATAATTCCCGcccccgcgacgcc                                                                            >  1:92863/1‑239 (MQ=255)                                                                                                                                                                  cctgtgggggttgtgtttgCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTTCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCt                                                                          <  2:53468/234‑1 (MQ=255)                                                                                                                                                                          gATTTTTTTTGCTGTGGGGCGTAAGGCAGCGGTGCTAGCTTTTTTGTGCGTTGTTTCAATATTCTGGTGGCGGTCTGCTCTCTCGGTACGATGTCGCTTTCGCCTTACACCGTGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCTGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTTCCGCTTATTGCGTg                                                                 <  2:270870/251‑1 (MQ=255)                                                                                                                                                                                       ggtggGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTGGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTc                                                     <  2:234887/250‑1 (MQ=255)                                                                                                                                                                                             cGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCTGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGAAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCACCTGCGTACCGCTTATTGCGTGACGGCTGCCGTCAATcccc                                              >  1:22181/1‑248 (MQ=255)                                                                                                                                                                                                                                    atatGCTGGTGGCGGTCTGCTCTCCCGGGACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAAATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGAt       >  2:95307/1‑251 (MQ=255)                                                                                                                                                                                                                                           ggtggCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATGGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGATTCCGa  <  1:116221/249‑1 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                               AATCAGATGATGCGGATCGTCGGCTGGCATACCGCAGCAAGCACACGGCTGTGTCTTAACCCAACGTGTGTATTTCTCCTTAACCCAGCGGCGACGTTTAGGCAGCTTCATGAAAGATTCCGGAGACTCTGGATCAACGGTGATGCTTACCACCGTCTTTTCCTGTGGTGATTTTTGTTGCTGGTGGGCGTAAGGCAACGGTGCAAGATTTTTTGTGCGTTGTTTCAATATGCTGGTGGCGGTCAGCTCTCCCGGTACGATGTCGCTTTCGCGGTACACCGAGCAGATTTTTTCCGCTGGTAATCCCAGCGAACGACGCGATACAGCCTCAGGTAGTGCATCCACCACCTGATTGCAGACCGCCCACCAGGATAATTCAGCCAAAGATAATTCCCGCTCCTGCGTACCGCTTATTGCGTGACGGATGACGTCAATCACCCATGCTGTCAGATTTTGTTGAGCAAGCAGCTCCAGTGATTCCGA  >  NC_000913/1643435‑1643917

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: ‑