Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	5,183	A→C	intergenic (+163/‑51)	thrC → / → yaaX	threonine synthase/DUF2502 domain‑containing protein YaaX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	5,183	0	A	C	82.3%	29.6 / 1.4	17	intergenic (+163/‑51)	thrC/yaaX	threonine synthase/DUF2502 domain‑containing protein YaaX
Reads supporting (aligned to +/- strand):  ref base A (3/0);  new base C (5/9);  total (8/9)
Fisher's exact test for biased strand distribution p-value = 8.24e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.11e-01

TTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGC  >  NC_000913/4949‑5428                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                      ttACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                                                                                                                                                                                                                       >  1:211714/1‑251 (MQ=255)                                 ttttGCTGCGTTGCGTAAATTGATGTTGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCC‑GGCTTTTTTATGAAGAAATTATGGAGAAAAACGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATTGACCCCTAACGGGCAATGATAAAAGGAGTAAcc                                                                                                                                                                                                      >  1:269373/1‑251 (MQ=255)                                                                   caGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCC‑GTCTTTTTTATGAAGAAATTATGGAGAAAAACGACAG‑GGAAAAAGTAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTCTGAAAAAGATGCAATCTATCGTACTCGCACtt                                                                                                                                                                    <  1:213204/251‑1 (MQ=255)                                                                            cTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATCCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGt                                                                                                                                                            >  1:22063/1‑251 (MQ=255)                                                                                   gtATCCCAATTAGGCCGGGTTTGCCGTTATGTA‑TCCAGTTTTTATATGAAGAAATTATGGAGAAAAACGA‑AGTGTAAAAAGGA‑AAATTTTGCAATAATTGCGGTAACGTCGAGATTAAGACTGAGGATAATAACAACCGGCGTTGTCATTTCGGAATCTCCTGATAGCGTGGCGTATCGTGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATATAGCGTACTCTCACTTTCCCTGGTTCtt                                                                                                                                                        <  2:220562/246‑2 (MQ=255)                                                                                           aTCAGGCCGGGTTTGCTTTTGTGCAGCC‑GGCTTTTTTATGAAGAAATTATGGAGAAAAACGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATg                                                                                                                                            <  1:10166/251‑1 (MQ=255)                                                                                                                                tATGAAGAAATTATGGAGAAAAACGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTc                                                                                                         <  1:211156/250‑1 (MQ=255)                                                                                                                                       aaaTTATGGAGAAAAACGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAAt                                                                                                 <  1:85658/251‑1 (MQ=255)                                                                                                                                            aTGGAGAAAAATGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAGTGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTACGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCACTGGTACTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATACCGTTAGTCCAGTAAGTAAAATTAc                                                                                              >  2:155065/1‑249 (MQ=255)                                                                                                                                                 gaAAAACGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGGCCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAgg                                                                                       <  1:35345/251‑1 (MQ=255)                                                                                                                                                                             tct‑cAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAAGCTATCGTTCTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACt                                                             <  1:380565/250‑1 (MQ=255)                                                                                                                                                                              ct‑cAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTgg                                                           >  1:14131/1‑251 (MQ=255)                                                                                                                                                                                                           ggATTGCGGAGAATAACAACCGTCGTTCTCATCGCGTAATCTCCGGATATCGACACATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCACTGGTTCTGGTCGCTCCCATGGCAGAACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATAGTGGCTATTACTGGGATGGAGGTCACAGGCGCGACCACGGCt                               >  1:72185/1‑251 (MQ=255)                                                                                                                                                                                                            gtgtGCGGAGCATAACAACCGGCGTTCTCATCGCGTAATCTCCAGATATCGACCCATAACGGGCAATCAGAAAAGGAGTAACCTATGAAAAAGATGCAATCGATCGTACTCGCACTTTCCCTGTTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGTCGATCGTTATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCtg                              <  2:197684/248‑1 (MQ=255)                                                                                                                                                                                                               tGCGGAGAATAACAACCGTCGTTCTCATCGCGAAATCTCCGGATATCGAACCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAATATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTAGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTAAGTAAAATTACAGATATGCGATCGTGATAACAGTGGCGATTAATGGGATGGAGTTCACTGGCGCGACCACGGCtgggg                           >  2:274553/1‑249 (MQ=255)                                                                                                                                                                                                                         aacaacCGTCGTTCTCATCGCGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTATGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACAt                 <  1:88561/251‑1 (MQ=255)                                                                                                                                                                                                                                         aTCGCGTAATATCCGGATATCGACACATAACGGGCCATGATCAAAGGAGTAACCTATGAAACAGATGCAATCTATCGTACTCGCACTTTTCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGAAAAATTACAGATAGGCGATCGTGCTCATCGTTGCTATTTCTGTAATGGAGGTCACTGGCGCGACCACGGCTGGTGGGAACAACATTATAAATgactagga  >  1:206929/1‑243 (MQ=255)                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                                      TTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAG‑GGAAAAAGGAGAAATTCT‑CAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTCCCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCGACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGC  >  NC_000913/4949‑5428

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑