Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,411,689	G→T	E13* (GAA→TAA)	yhdJ →	DNA adenine methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,411,689	0	G	T	87.5%	33.9 / NA	16	E13* (GAA→TAA)	yhdJ	DNA adenine methyltransferase
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base T (8/6);  total (8/8)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAATACACCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGAACAGTACGGAAAACATGC  >  NC_000913/3411472‑3411926                                                                                                                                                                                                                          |                                                                                                                                                                                                                                              cAATACACCCGTGGTAACCAGACCCGTGCTGCGCTGAGGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCAAAATGCGTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGGGACCATGAGAACAGGATGTGATCCGACCCGGTGTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCttn                                                                                                                                                                                                              <  1:34019/251‑2 (MQ=255)     acacCCGTGGTAATCAGACCCGTTCTGCGCTGATGAATGGCAACAACCGTGGTTCGCTGCGTAAAAAATGGAAAAAAGACGGCATTAGCTAACGCAGGTTAGCTAAATGCTTGATTAAAAAGGGGCTACACGGGAGGGGGAAGCGCCTTGTTTATAGTTGGCAGAAAGGTAGTGAGGATGAGAGCAGGATGGGAAGGGAGCCGGTTTGGTAATGAATCTAGGAACTTTATTGACGGTGATGCGCTTGCCGa                                                                                                                                                                                                          <  1:139465/251‑1 (MQ=255)          cGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAAACGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGCAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACtt                                                                                                                                                                                                      >  1:199879/1‑250 (MQ=255)                                   tgaggatggtaaTCAACGGTGGTACGTGGCGAAAAAAATTGAAAAAATACGGCATGAACTAATTCAGTTTAGCTAAAGGCTTTATTAAAAAGGCGCTACTGGGCATGGGGAAGCGCCTTTTTTATGGGTGTCACAAAGGGAGTTACAATGAGAAAAGGAGGTGAACCGCCGCGGTTGGGTATTTAAGCTAAGCCCTTTATTACCGGTGAGCCGCTCGCCCAACTTAAAAAGAACCCCGTCGAAAGTGTCg                                                                                                                                                                             <  1:129458/239‑1 (MQ=255)                                                            gCTGCATAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGc                                                                                                                                                                >  1:145027/1‑238 (MQ=255)                                                                  tAAAAAATTGAAAAAATCCGGCATGAACTAATTCAGGTTAGCTAAATGCTTGCTTAAAAAGGCGCTACTCGGCCTGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGc                                                                                                                                                                                                             >  1:338709/1‑187 (MQ=255)                                                                                                          gCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAACCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCgatctga                                                                                                                                                                       >  1:242230/1‑185 (MQ=255)                                                                                                          gCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACAGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAAtttt                                                                                                                                 >  1:306640/1‑223 (MQ=255)                                                                                                                                            tGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGACCCGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTg                                                                                                                                                                                                              <  1:28178/112‑1 (MQ=255)                                                                                                                                                  cgcgcCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTg                                                             >  1:100059/2‑251 (MQ=255)                                                                                                                                                     gcCTTGTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGt                                                                                                                                                                                                                        <  1:140158/93‑1 (MQ=255)                                                                                                                                                                               aGTGACCATGAGAACAGGAGGTGAACCGACCCGGTTTGGTAATTAAGCTAAGACCTTTATGCACGGTGATGCGCTTGCCGAACTAAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTAGCGACTTGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGgcagca                                <  1:143437/251‑1 (MQ=255)                                                                                                                                                                                                          tccccGGTTTGGTAAGTAAGCTAATCCCAGTATTCTCGGTGATGCGCTGGCTGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTGTGCCGACCCAGCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAg                                                                                                                 <  1:262129/141‑1 (MQ=255)                                                                                                                                                                                                          gACCCNNTTNNNTANNTCAGCTAAGACCATTATTCACGGNGATGCGCTTGCCGAACTTAAAAAGATCCCNGNCNAAAGNNTCGNTCTGATCTTTNCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAg                                                                                                                 >  2:262129/1‑143 (MQ=255)                                                                                                                                                                                                             ccGGTTGGGTAAGGAAGCTAAGACCATTATCCACGTTGATGCGCTTGCCGAACTTAAAAAGATCACCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGAACAGTACGGAAAACATgn  <  1:221936/251‑2 (MQ=255)                                                                                                                                                                                                                    ggTAATTAAGCTAAGACCATTATTCACGGTCATGCGCTTGCCGAACTTAAACAGCTCAACGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATc                                                                                                  >  1:139910/1‑148 (MQ=255)                                                                                                                                                                                                                          |                                                                                                                                                                                                                                              CAATACACCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGACCCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGAACAGTACGGAAAACATGC  >  NC_000913/3411472‑3411926

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑