Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AE015451	1,499,480	2 bp→AC	intergenic (+57/‑106)	trpS → / → zapE	Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	1,499,480	0	C	A	95.7%	69.1 / ‑4.0	23	intergenic (+57/‑107)	trpS/zapE	Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (11/11);  minor base G (1/0);  total (12/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01
*	AE015451	1,499,481	0	A	C	95.7%	72.3 / ‑5.4	23	intergenic (+58/‑106)	trpS/zapE	Tryptophan‑‑tRNA ligase/putative enzyme with nucleoside triphosphate hydrolase domain
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base C (12/10);  total (12/11)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

AGCTTCGCCGACGGCAAGAGT‑GCTGGCGCCGTGAGCAAGCAGCTGCAGCAAGGTGGCGAGGCCGATGTCCGCATCGAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGACCTGGTGCACGCGCAGAACAACAAGCCGGGCATGTTCGGCAAGCTGTTCGGCAAGAAGGAGCAGACTCCGGTCA  >  AE015451/1499220‑1499764                                                                                                                                                                                                                                                                      ||                                                                                                                                                                                                                                                                                               cgCTTCGCCGACGGCAA‑TGTGGCTTGCGCCGTGAGCAAGCAGCTGCAGCAAGGTGGCGAGCCCGATGTCCGCATCGAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAg                                                                                                                                                                                                                                                         <  2:118361/300‑1 (MQ=255)               cAAGAGT‑GCTGGCGCCGTGAGCAAGCAGCTGCAGCAAGGTGGCGAGGCCGATGTCCGCATCGAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCATAGACTGATTGCCacta                                                                                                                                                                                                                                           >  1:575281/1‑298 (MQ=255)                    gggggtgggggcgtgggcaggcggggggagcaAGGTGGCGAGGCCGATGTCCGCATCGAAGGCCTGAGCTGCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGCAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCTCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCg                                                                                                                                                                                                                                       <  2:513091/273‑1 (MQ=255)                                                 gcaAGGTGGCGGGGCCGATGTCCGCATCGAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGtttt                                                                                                                                                                                                          <  1:183994/301‑1 (MQ=255)                                                                  aTGTCCGCATCGAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCAGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCCTTATGCGGGCCTACCGCTACAGTGACGGTCCGTTTTTTGTTGCCTCGCTCACg                                                                                                                                                                                         >  1:306010/1‑301 (MQ=255)                                                                     tCCGCATCGAAGGACTGAGCTTCGGCCTGTGGCTCAATGGCGGGCAGGTTGCCGACGGCCCGCAGTTCGACAACGCTGAAGCGCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAAt                                                                                                                                                                                      <  1:545828/301‑1 (MQ=255)                                                                        gaaTCGAAGGCCTGAGGTGCGGGCGGTGGCGGAAGGGGGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCGGTGATGCGGCCATTCAGAGGCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGGGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTCCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCAt                                                                                                                                                                                   <  2:638697/299‑1 (MQ=255)                                                                             gAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTCAGCGGGCCTATCGCTACAGTTACGGCCCGTTTTTTGTTGCCTCGCCAACGAATCCTGACTc                                                                                                                                                                              >  1:287212/1‑301 (MQ=255)                                                                                  ccTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCCCGCCAACGAATCATGACTCCCttt                                                                                                                                                                         >  1:350354/1‑300 (MQ=255)                                                                                                             cGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGGGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGGACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGCTTTCCATTAAGCGGGCCTATCGCCACAGTGACGGCCCGTTTTTTGGTGCCTCGCTTACGAATTCTGACGCCCTTCAG‑ACGCCCTCCAACAGATCTGAAACGt                                                                                                                                             >  2:664321/1‑301 (MQ=255)                                                                                                              gggagggTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGACCGGGATGCGGCCAGTGAGAGACTGAACGAAGCCGTGGCACCACAGCAGGACTGAGGCTGGCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTc                                                                                                                                            <  2:491236/296‑1 (MQ=255)                                                                                                                     ttGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTCATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCAACGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGActt                                                                                                                                     <  1:337073/301‑1 (MQ=255)                                                                                                                                    aGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCCACAGTGACGGCCCGTTTTTTGTTGCCTTGCCAACGAATCATCACCGCCTT‑AGAACGCTATCAACCAAAACTGAAAAGTCCCGACTTCTTCCATTACccggc                                                                                                                      >  2:513461/1‑301 (MQ=255)                                                                                                                                                     gCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGc                                                                                                     <  1:513669/301‑1 (MQ=255)                                                                                                                                                         gTGATGCGGCCATTCAGGGCCTGAGCGAAGCCGTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGATGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCa                                                                                                 <  1:743719/301‑1 (MQ=255)                                                                                                                                                                  ccATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCCCCCACAGACTGATTGCCATTAAGCGGGCCGATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTTACGAATCCTGACTCCCTT‑ATCACGCTATCAAGCAGATCTTAAACGTCCCGACTTCTTACATGACGCGGCGCAGGAAACTGCGGGGCTTCACCCCCaacc                                                                                        >  2:549140/1‑298 (MQ=255)                                                                                                                                                                                  agAAGCCTTGGCACCCAAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGACCTg                                                                        <  1:736945/300‑1 (MQ=255)                                                                                                                                                                                                   agcagGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCGCCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATTACGCGGCGCAGGAAACTGCGGTGCGGCACCTCCAGCGCCTGTACGACGACCTGGTGCAcgctgaagacaa                                                       >  1:273860/1‑292 (MQ=255)                                                                                                                                                                                                                  gCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCCTGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGACCTGGTGAACGCGCAGAACAACAAGCCGGGCATGtt                                        >  1:33281/1‑301 (MQ=255)                                                                                                                                                                                                                             ggAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTCCGACGACCTGGTGCACGCGCAGCACAACAAGCCGGGCATGTTCggaacgatgt                             >  2:142671/1‑293 (MQ=255)                                                                                                                                                                                                                                                   aggggccgcGGTGCATGGCACCGGCTTTGCCGGTGTTCGGGGGCACGCCCGCTCCCACAGACTGATGGCCATTAAGCGGGCCTATCGCTACAGTGACGGCACGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGACCTGGTGCACGCGCAGAACAACAAGCCGGGCATGTTCGGCAAGCTGTTCGGCAAGAAGGAGCAGACTcc       <  1:144752/297‑1 (MQ=255)                                                                                                                                                                                                                                                   aGGCGCCGCGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACCCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGATCTGGTGCACTCGCAGAACAACAAGCCTGGCATGTTCGGCAAGTCGTTCGGCCAGAAGTCGCAGACTcc       >  2:144683/1‑301 (MQ=255)                                                                                                                                                                                                                                                        ccgcGGTGCATGGCACCGGCTTTGCCGGTGTTCGCGGGCACGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCCTGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGACCTGGTGCACGGGCAGAACAACAAGCCGGGCATGTTCGGCAAGCTGGTAGGCAAGAAGGCGCAGACtgccgaca  >  2:63195/1‑294 (MQ=255)                                                                                                                                                                                                                                                                      ||                                                                                                                                                                                                                                                                                               AGCTTCGCCGACGGCAAGAGT‑GCTGGCGCCGTGAGCAAGCAGCTGCAGCAAGGTGGCGAGGCCGATGTCCGCATCGAAGGCCTGAGCTTCGGCCTGTGGCTCAATGGCGAGCAGGTTGCCGACGGGCCGCAGTTCGACAACGCTGAAGCCCGTGATGCGGCCATTCAGAGCCTGAACGAAGCCTTGGCACCACAGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCACGGCTTTGCCGGTGTT‑TCGGGCACG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTT‑AGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGACGCGGCGCAGGAAACTGCGGTGCGTCACCTCCAGCGCCTGTACGACGACCTGGTGCACGCGCAGAACAACAAGCCGGGCATGTTCGGCAAGCTGTTCGGCAAGAAGGAGCAGACTCCGGTCA  >  AE015451/1499220‑1499764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑