Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,400,119	G→A	E290K (GAA→AAA)	miaA →	tRNA dimethylallyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,400,119	0	G	A	90.0%	46.3 / NA	20	E290K (GAA→AAA)	miaA	tRNA dimethylallyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (7/11);  minor base C (2/0);  total (9/11)
Fisher's exact test for biased strand distribution p-value = 1.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

CAGCGTTTTCATCAGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCG  >  NC_000913/4399897‑4400337                                                                                                                                                                                                                               |                                                                                                                                                                                                                           cagcGTTTTCATCAGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGaaa                                                                                                                                                                                                 >  1:363871/1‑250 (MQ=255)                             gTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGc                                                                                                                                                                                                             <  1:352994/210‑1 (MQ=255)                                       aGAAGTCGGGGCGCTGTTTGCCCGAGGAGATTTGCATACGGACTTGACGTCCATTCGTTGCGTGGGTTATCGCCAGAGGTGGTCTTACCGTGAAGGCGAAAGCTCAGTCGATGAAGTGGGTGATCGAGGTGTTTGCGCTAAGAGTCAGTGGTCGAAGTGGCAGAGAACCTGGCTTCGGGGTTGGAAAGGGGGTAACTGGCTTGACAGTGAAAAACCCGAACAGGCGCGTGACGAAGTATTACAGGttgttg                                                                                                                                                          <  1:236736/251‑1 (MQ=255)                                                 gcgcTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTGCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCgn                                                                                                                                                <  1:263513/251‑2 (MQ=255)                                                                ggagATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGCTGTGGTCTTACCTTGAAGGCGAGATCTCATACGATGTCATGGTTTATCGAGGTGTTTGCGCCACGAGCCAGTTGGCGAAGCGGCCGCTCACCTGGCTGCGTGGTTGGACCGGGGTTCACTGGCTTGACCGTGAAAAACCCGAACAGTCGCGTGACGCAGTCTTCCAGTTTGTTGGTTCTCTCGCAGGCTGACTGTGTAc                                                                                                                                 >  1:262246/1‑251 (MQ=255)                                                                                                    gTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTGATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGGTGTTGGTGCTATCGCAGGCTGAATGTGTGCAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCg                                                                                             <  1:177586/251‑1 (MQ=255)                                                                                                                       ggTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTgn                                                                                                               <  1:81405/214‑2 (MQ=255)                                                                                                                                         aaaTCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATACCCTGGCTGAGTGGTTGGCAAGGGGTTCACTGGCTTGACAGTGAAAAACAAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTgg                                                                                                                                                         >  1:429010/1‑154 (MQ=255)                                                                                                                                                                         gtTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGCAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCtttcca                             >  1:380698/1‑243 (MQ=255)                                                                                                                                                                             gcgcCACGAGACAGGTGGCGAAGCGGCAGAGAACCTGGCTGCGTGGTTGGAAAGGGGTTCACGGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTAGTACAGGTTGTTGGTGCTATCGCAGGCTGAATGCGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTAc                                                                              <  1:172684/193‑1 (MQ=255)                                                                                                                                                                              cgcCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCa                                                                                                   >  1:248787/1‑171 (MQ=255)                                                                                                                                                                                ccACGNNACNNNTGNNGAAGCGGCAGATAACCTGGCTGCNTGGTTGGAAAGGGGTTCACTGGCTTGACANTNANAAACNNGAANAGGCGCGTGANGAAGTATTACAGGTTGTTgg                                                                                                                                                         >  2:338051/1‑115 (MQ=255)                                                                                                                                                                                ccACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTAGTACAGGTTGTTgg                                                                                                                                                         <  1:338051/115‑1 (MQ=255)                                                                                                                                                                                ccACGAGACAGTTGGCGAAGCGGCAGATAACATGGCTGCGTGGTTGGAAAGGGGTTCACTGGATTGCCAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTgc                                                                                                               >  1:168368/1‑157 (MQ=255)                                                                                                                                                                                     agaCAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACg            <  1:201747/251‑1 (MQ=255)                                                                                                                                                                                               cGAAGCGGCAGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGc                                                                                                                                                      <  1:392623/103‑1 (MQ=255)                                                                                                                                                                                                        aGATAACCTGGCTGCGTGGTTGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTgcgc                                                                                                             >  1:163242/1‑135 (MQ=255)                                                                                                                                                                                                               cTGGCTGCGTGGATGGAAAGGGGTTACCTGGCTTGCCAGTGAAAAACCAGAACAGGCGAGTGACGAAGTATTACAGGCTGTTGGTGCTATCGCAGGCTGAATGGGTACAATTGAGACGTATCGTGCGAACTTTTTTCAGAATCGAAAGGATCAAAGTACAAATAAGCATATAAGGAACCGAGCGCATGGATAAGGGGCAATCTTTACAAGATCCGTTCCTGAAc             >  1:179706/1‑224 (MQ=255)                                                                                                                                                                                                                        tGGTTGGAAAGGGGTTCACTGGCGTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAAGTGAGACGTATCGTGCGCAATTTTTTCATAATCGAAAGGTTCAAAGTACAAATAAGCATAGAAGGAAAAGAGAGAATGGCTAAGTGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCg  <  1:65008/226‑1 (MQ=255)                                                                                                                                                                                                                           ttGGAAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGc      <  1:102140/219‑1 (MQ=255)                                                                                                                                                                                                                               |                                                                                                                                                                                                                           CAGCGTTTTCATCAGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCATACGATGAAATGGTTTATCGAGGTGTTTGCGCCACGAGACAGTTGGCGAAGCGGCAGATAACCTGGCTGCGTGGTTGGGAAGGGGTTCACTGGCTTGACAGTGAAAAACCAGAACAGGCGCGTGACGAAGTATTACAGGTTGTTGGTGCTATCGCAGGCTGAATGTGTACAATTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAGGTTCAAAGTACAAATAAGCATATAAGGAAAAGAGAGAATGGCTAAGGGGCAATCTTTACAAGATCCGTTCCTGAACGCACTGCGTCG  >  NC_000913/4399897‑4400337

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑