Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,967,770	C→T	intergenic (+94/‑146)	rho → / → rfe	transcription termination factor Rho/UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,967,770	0	C	T	94.4%	49.0 / ‑5.9	18	intergenic (+94/‑146)	rho/rfe	transcription termination factor Rho/UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (9/8);  total (10/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGCTCACGACTCAGGAAGAACTGCAGAAAATGT‑GGATCCTGCGCAAAATCATTCACCCGATGGGCGAAATCGATGCAATGGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCCTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCTCATCAGTATTTTTTTATTCACGACACTGTTTCTGTTTTTTGCCCGTA  >  NC_000913/3967523‑3967991                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                gctgctCACGACTCAGGAAGAACTGCAGAAAATGT‑GGATCCTGCGCAAAATCATTCACCCGATGGGCGAAATCGATGCAATGGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAAGCTTAATGCCGCGCTGGCGAGGTTGGGAAAATTCTTgg                                                                                                                                                                                                                              <  1:311634/251‑1 (MQ=255)                 gaagaaCGGCAGAAAATGTTGGA‑CATGAGAAAAATCATTCACCCGATGGGCAGAATCGATGCAATTGATGTCCTCATTAATAAACTGGCAAGTACCCAGACCAATGACGAGTTCTTCGAAATGATTAATCGCTCATAAATTTGTTGTATGCGAAAAACGGCGCGTGTTTACGTGGCGGTTGTATTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGGGAGGAAAATTCTGGGA‑TTTTGCTGGCATGtt                                                                                                                                                                                                             <  2:161505/251‑1 (MQ=255)                    gaaCTGCAGAAAATGT‑GGATCCTGCGCAAAATCATTCACCCGATGGGCGAAATCGATGCAATGGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATg                                                                                                                                                                                                          >  1:277759/1‑251 (MQ=255)                              aaaaagaggATCCTGAGAAAAATCATTCACACGATGGGGGAAATCGATGCAATGGAATTCCTCATTAATAAACTGGAAATGACCAAGACAAATGAGGATTTCTTCGAAATGATTAATAGCTAATAAATTAGTCTTATTCCAAAAACGCCACACGATTACGTGGCGTTTAGCTTTTATATCTGTAATCTTAATGCCGCGCTGACGATGTTAGTAAAAT‑GCTAGATATTTGCTGGCGTGTTAAGCAAtattat                                                                                                                                                                                                 >  2:83794/8‑246 (MQ=255)                                             cgcAAAATCATTCACTCGATGGGCGAAATCGAGGCAATTGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAAt                                                                                                                                                                                  <  1:92888/251‑1 (MQ=255)                                                                      aaaTCGATGCAATGGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTgg                                                                                                                                                         >  1:78341/1‑251 (MQ=255)                                                                                aaTGGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACttt                                                                                                                                              <  1:384089/251‑1 (MQ=255)                                                                                                    aaCTGGCAATGACCAAAACCAAGGACGATTTCTTCGAAATGAAGAAACGCTCATAAATCTGTCTTATGCCTACAACGCCACGAGTTTACGTGGCGTTTTGCTTTTATATCTGTAATATTAATGCCGCGCTCGCGATGTTAGGCAAATTCTTGGT‑GTTTGTTGGCATGTTATGCTATTTGCATTACATATGGTTCATTTTTGCTCAGGACTTGTGGGGTTGTACCGTGA‑TTTACCTTCTGAATaacaggctt                                                                                                                          >  2:91318/1‑244 (MQ=255)                                                                                                             tGACCAAGCCCACTGGAGATTTCTTCGAAATGATGAAACGCTCTTAAATTTGTCTTACGCCAAAAACGCCACGCGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTATTGGC‑ATTTGCTGGCATGTTATGCAATTTGCCTATCACATGATTAATTTTTGCACAGGCCTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGACTAAAGGTCTTCGTGGTtat                                                                                                                 >  2:380845/1‑251 (MQ=255)                                                                                                                           gACGATTTCTTCGAAATGATGAAACGCTCATACATTTGACTTATGCCAAATAAGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGTTGTTAGGAAAATTCTTGGA‑ATTTACTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GATTTTCCCTTCTGCATAAAGATATTCGAGGTTATAATTCTGCtcata                                                                                                    >  2:60184/1‑250 (MQ=255)                                                                                                                             cGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTACCTTCTGAATAAATGTCTTCGTGGTTATACTTCTGCTAATAAtt                                                                                                 >  1:155657/1‑251 (MQ=255)                                                                                                                              gATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAACCGCCACGAGTTTACATGGCGTTTTGCTTTTATATCTGTAATCTTACTGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATTGTTAATTTTTTCCCAGGACTGGAGGGTTTGGAACT‑GAATTTCCCTTCTGGATAAAGGTATTCGTGGGTATACTGTTGCTAATAAttt                                                                                                >  2:101739/1‑251 (MQ=255)                                                                                                                                            gatgaAACGCTCATAAATGTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCGCAGGACTGGTGGGTTTGGAACG‑GACTTGCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTGCTCTGAGAgcat                                                                                   <  1:380845/250‑1 (MQ=255)                                                                                                                                                                                       gtTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCTCATCGGTAtt                                       >  1:73621/1‑251 (MQ=255)                                                                                                                                                                                                             atatCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCTCATCAGTATTTTTTTATTCACGACActgttt                  <  1:360781/250‑1 (MQ=255)                                                                                                                                                                                                                         ttAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCtcat                                              <  2:174014/210‑1 (MQ=255)                                                                                                                                                                                                                         ttAATGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCtcat                                              >  1:174014/1‑210 (MQ=255)                                                                                                                                                                                                                            aTGCCGCGCTGGCGATGTTAGGAAAATTCTTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCTCATCAGTATTTTTTTATTCACGACACTGTTTCTGTTTTTTGCCCGTa  <  1:284813/251‑1 (MQ=255)                                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                GCTGCTCACGACTCAGGAAGAACTGCAGAAAATGT‑GGATCCTGCGCAAAATCATTCACCCGATGGGCGAAATCGATGCAATGGAATTCCTCATTAATAAACTGGCAATGACCAAGACCAATGACGATTTCTTCGAAATGATGAAACGCTCATAAATTTGTCTTATGCCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAATTCCTGGA‑ATTTGCTGGCATGTTATGCAATTTGCATATCAAATGGTTAATTTTTGCACAGGACTGGTGGGTTTGGAACG‑GACTTTCCCTTCTGAATAAAGGTCTTCGTGGTTATACTTCTGCTAATAATTTTCTCTGAGAGCATGCATTGTGAATTTACTGACAGTGAGTACTGATCTCATCAGTATTTTTTTATTCACGACACTGTTTCTGTTTTTTGCCCGTA  >  NC_000913/3967523‑3967991

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑