Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,883,195	C→T	12.1%	P369L (CCG→CTG)	tnaA →	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,883,195	0	C	T	12.1%	73.8 / 3.0	33	P369L (CCG→CTG)	tnaA	tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent
Reads supporting (aligned to +/- strand):  ref base C (15/14);  new base T (2/2);  total (17/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01

GTCTGTATGACGGCATGAATCTCGACTGGCTGGCTTATCGTATCGCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAAACAACTGCCATGCCCGGCT  >  CP009273/3883051‑3883334                                                                                                                                                 |                                                                                                                                            gTCTGTATGACGGCATGAATCTCGACTGGCTGGCTTATCGTATCGCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCat                                                                                                                                         >  1:306049/1‑149 (MQ=255)     gTATGACGGCATGAATCTCGACTGGCTGGCTTATCGTATCGCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGc                                                                                                                                           <  2:171410/143‑1 (MQ=255)                       ggACTGGCTGGCTGATCGTATCGCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCgg                                                                                                                   <  1:390745/148‑1 (MQ=255)                           tggttggcTTATCGTATCGCGCAGGTACAGTATCTGGTCGATGGGCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTccc                                                                                                                     <  2:404402/143‑1 (MQ=255)                             gctggctTATCGTATCGCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCgg                                                                                                                   <  2:349577/143‑1 (MQ=255)                                         tttcgCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGAGGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCg                                                                                                 <  1:440242/147‑1 (MQ=255)                                         tatcgCGCAGGTACAGTATCGGGACGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTgg                                                                                                       >  2:236291/1‑143 (MQ=255)                                             gcgcAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCTGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGGGAGCt                                                                                             >  1:145011/1‑149 (MQ=255)                                             gcgcAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCTGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCt                                                                                             >  1:460557/1‑149 (MQ=255)                                               gcAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGt                                                                                           <  1:108807/149‑1 (MQ=255)                                               gcAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGt                                                                                           >  1:22422/1‑149 (MQ=255)                                                   gTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGCGCt                                                                                             >  2:34255/1‑143 (MQ=255)                                                   gTACAGTATCTGGTCGATGGTCTGGAAGAGATTGCAGTTGTCTGCCAGCACGAGGGCGGTCACGCGGCGTTCGTTGATGGCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGCGACAAGCGCTGGGCTCCgcgcc                                                                                             >  2:292761/1‑142 (MQ=255)                                                   gTACAGTATCTGGTAGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCGCGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCt                                                                                             >  2:87229/1‑143 (MQ=255)                                                                 cGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCg                                                                               >  2:279046/1‑143 (MQ=255)                                                                              gagaTTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGt                                                                  >  2:253039/1‑143 (MQ=255)                                                                                   gggCGGTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGaaa                                                             <  2:1539/142‑1 (MQ=255)                                                                                            cTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCtt                                                    >  2:145454/1‑143 (MQ=255)                                                                                               ccAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAg                                           >  1:102691/1‑149 (MQ=255)                                                                                                 agcagGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTg                                               >  2:301025/1‑143 (MQ=255)                                                                                                   cacgcgggcggTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCcg                                       <  1:393996/146‑1 (MQ=255)                                                                                                      gcgggcggTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCTGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAgg                                          <  2:414579/143‑1 (MQ=255)                                                                                                      gcgggcggTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCTGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAgg                                          <  2:129279/143‑1 (MQ=255)                                                                                                       cgggcggTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAAGc                                         >  2:467227/1‑143 (MQ=255)                                                                                                              tCACGCGGCAGTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGaaaa                            >  1:506535/1‑149 (MQ=255)                                                                                                                acggcgCATTCGTTGATGCCGGTAAACTGTGGCCGCATAGCCCGGCAGCCCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCg                                <  2:242323/138‑1 (MQ=255)                                                                                                                 cgcgGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGa                               <  2:389247/143‑1 (MQ=255)                                                                                                                         tCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAaacaa                 <  1:495837/149‑1 (MQ=255)                                                                                                                         tCGTTGAGGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAaacaa                 <  1:260019/149‑1 (MQ=255)                                                                                                                               aTGCCGGTAAACTGTTGCCGCATGTCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAAACAACTGCCa           >  1:278175/1‑149 (MQ=255)                                                                                                                                  ccGGTAAACTGTTGCCGCATACCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAAACAACTGCCATGc        <  1:87199/149‑1 (MQ=255)                                                                                                                                       aaaCTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTCTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAAACAACTGCCATGCCCGGc   <  1:274821/149‑1 (MQ=255)                                                                                                                                              tGCCGCATATCCAGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAAACAAATGCCATGCCCGGCt  >  2:363146/1‑143 (MQ=255)                                                                                                                                                 |                                                                                                                                            GTCTGTATGACGGCATGAATCTCGACTGGCTGGCTTATCGTATCGCGCAGGTACAGTATCTGGTCGATGGTCTGGAAGAGATTGGCGTTGTCTGCCAGCAGGCGGGCGGTCACGCGGCATTCGTTGATGCCGGTAAACTGTTGCCGCATATCCCGGCAGACCAGTTCCCGGCACAGGCGCTGGCCTGCGAGCTGTATAAAGTCGCCGGTATCCGTGCGGTAGAAATTGGCTCTTTCCTGTTAGGCCGCGATCCGAAAACCGGTAAACAACTGCCATGCCCGGCT  >  CP009273/3883051‑3883334

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑