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	84.0%	43.4 / 4.7	25	E13* (GAA→TAA)	yhdJ	DNA adenine methyltransferase
Reads supporting (aligned to +/- strand):  ref base G (3/1);  new base T (12/9);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 6.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.34e-01

GTAGAACAGCCCCTGTTGGACATGGTGATGCAATACACCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGAACAGTACGGAAAACATGCC  >  NC_000913/3411442‑3411927                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                               gTAGAACAGCCCCTTGTGGACAGGGTGATGCAATACACCCGTGGTAACCAGACCAGTGCTGCGCTGATGATTGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCATTTTTTATAGGTGTCACAAAGGGAGTGTCCATGAGAACAGGATGTGAACCGAC‑CCGGTGTGGTAATTAAg                                                                                                                                                                                                                                             <  2:160515/251‑1 (MQ=255)                     cATGGTGATGCAATACACCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACggg                                                                                                                                                                                                                         >  1:8119/1‑250 (MQ=255)                              tataTACACCCGTGGTAACCAGTCCCGTGCTGCGCTGATGATGGGCCTCAGCCGTGGTACGCTTCGTAAAAAATAGAAAAAATTCGGCATGATCTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGAATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCt                                                                                                                                                                                                                 <  2:36397/247‑1 (MQ=255)                                    cacCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGaa                                                                                                                                                                                                          <  1:238965/251‑1 (MQ=255)                                     acCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTCAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAAGGAGTGACCATGAGAACAGGCTGTGAACCAAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGATTGCCGAAc                                                                                                                                                                                                         >  2:74327/1‑251 (MQ=255)                                       ccGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACtt                                                                                                                                                                                                       >  1:132278/1‑251 (MQ=255)                                              aaCCAGACCCGTGCTTCGCTGCTGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCACTACTCGGAATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGCC‑CCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGACCTTaaaacg                                                                                                                                                                                                 >  2:78010/1‑248 (MQ=255)                                                        gTGCTGCGCTGATGATGTGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGGTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAAATCCccgccgg                                                                                                                                                                                      >  2:66637/1‑250 (MQ=255)                                                               gcTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTc                                                                                                                                                                               <  1:78010/251‑1 (MQ=255)                                                                       tgGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACAGAC‑CCGGTTTGGTAATGAAGCTAAGACCATTATTCATGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCgatctgat                                                                                                                                                                       >  1:23986/1‑251 (MQ=255)                                                                           cATCAACCGGGGTACGCTGCGTAAAAAATTGAAAAAAACCGGCAGGAATTAATTCAGGTTATCTAAATGCTTAATTAAAAAGGCGCTACCCGGCTGGGGGACGCGCTTTTTTTATAGGTGTCACAAAGGGAGGGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTGGGTAATTAAGCTAAGACCATTTTTCACGGTGATGCGTTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCttt                                                                                                                                                                   <  2:74542/251‑1 (MQ=255)                                                                                             gCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCAGGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGACCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATaa                                                                                                                                                  <  1:90263/250‑1 (MQ=255)                                                                                                               aTACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCgatctgatc                                                                                                                                                                      >  1:7713/1‑212 (MQ=255)                                                                                                                           gtaaatCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCTGCCTGGGGAAGCGCCTTTTTTATAGGTGTAACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGAAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGAACTGATCTTTGCCGACCCACCATATAAACTCGGTAAAAATTTTGATGGTCTGATCGa                                                                                                                    >  2:226657/6‑250 (MQ=255)                                                                                                                             aaTTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCCGTAAAAATTTTGATGGTCTGATCGacgc                                                                                                                 >  1:11700/1‑248 (MQ=255)                                                                                                                               ttCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCGGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTAATGGTCTGATCGAAACCt                                                                                                               >  2:160614/1‑251 (MQ=255)                                                                                                                                 cAGGTAAGCTAAATGCGTTATTAAAAACGCTCTATTCGACAGGGGGGAGCGTGTTTTTTATAGGGGTCACAATGTGAGTATCCATTAGACCAGGCTGTGAACC‑ACACCGTTTGGGTAATTTAGCTAAGACCATTTGGCCCGGTGAGGCGTTTGCCGAACTTAACAAGCTCCCCGCCTAAAGTGTCGATCTGATCTTTGCCGACCCACCATATTACATCGGTAAAAATTTTGATGGTCTGATCGAATCCTgc                                                                                                             <  2:50341/251‑2 (MQ=255)                                                                                                                                        gCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGaatga                                                                                                        >  1:240462/1‑246 (MQ=255)                                                                                                                                               gCTTGATTAAAAAGGCGCTCCTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGtt                                                                                               <  1:74327/251‑1 (MQ=255)                                                                                                                                                                                           tataGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAACGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATATGTTTATCGAc                                                                                        >  2:235307/1‑214 (MQ=255)                                                                                                                                                                                           tataGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGAc                                                                                        <  1:235307/214‑1 (MQ=255)                                                                                                                                                                                              aGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTg                                                 >  1:174481/1‑250 (MQ=255)                                                                                                                                                                                                                          aCAGGATGTGAACCGCC‑CCGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGaa                    <  1:66637/251‑1 (MQ=255)                                                                                                                                                                                                                                       cGAC‑CCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGAACAGTACGGAAAAc       >  1:102551/1‑251 (MQ=255)                                                                                                                                                                                                                                             cGGTTTGGTAATTAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAACGCAGGGCAGCATGTACATCATGACCAGTACGGAAAACATGcc  >  1:288390/1‑251 (MQ=255)                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                               GTAGAACAGCCCCTGTTGGACATGGTGATGCAATACACCCGTGGTAACCAGACCCGTGCTGCGCTGATGATGGGCATCAACCGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGAACCGAC‑CCGGTTTGGTAATGAAGCTAAGACCATTATTCACGGTGATGCGCTTGCCGAACTTAAAAAGATCCCCGCCGAAAGTGTCGATCTGATCTTTGCCGACCCACCATATAACATCGGTAAAAATTTTGATGGTCTGATCGAAGCCTGGAAAGAAGATCTGTTTATCGACTGGCTGTTTGAAGTGATTGCAGAGTGCCACCGCGTTCTGAAAAAGCAGGGCAGCATGTACATCATGAACAGTACGGAAAACATGCC  >  NC_000913/3411442‑3411927

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑