Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	NC_000913	2,357,874	Δ12 bp	6.7%	pseudogene (59‑70/186 nt)	ypaA →	protein YpaA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2357873	54 (0.590)	4 (0.040)	4/276	NT	6.7%	pseudogene (58/186 nt)	ypaA	protein YpaA
	?	NC_000913	2357886 =	57 (0.620)					pseudogene (71/186 nt)	ypaA	protein YpaA

TTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2357813‑2357873 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGCCCACAGCCGATCCCCATGGG  >  NC_000913/2357886‑2358032                                                                                                                                                                                                                  TTAATGACTATTGCTGAACGGCTACGGCAGGAAGGGCATCAAATTGGCTGGCAGGAAGGTATGCATGAACAAGCCATTAAAATTGATTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCATGTGCTCGCGCCAACCAACCTAAcagaa                                                            >  1:1057505/1‑145  TAATGACTATTGCTGAACGGCTACGGCAGGAAGGGCATCAAATTGGCTGGCAGGAAGGTATGCATGAACAAGACATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACAAGGTGCTGGCGGCCAACCAGCTAAGCGAAc                                                           >  2:934429/1‑149                                                   tCAGGAAGGTATGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTG                                                                                                  <  2:70301/61‑1                                                   GCAGGAAGGTATGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTG                                                                                                  >  1:70301/1‑62                                                           GTATGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAGCAGGGCTTTGATCGTGACCATGTGCTCGCGGCCACCCAGCTAAGAGAAGCGGATATTGCGGCGAATAAGGACTAGGTAACACAGGACCCGAGCCGATCCCCATGGG  >  1:633229/1‑150                                                                                                                                                                                                                  TTAATGACTATTGCTGAACGGCTGCGGCAGGAAGGACATCAAATTGGCTGGCAGGAAGGTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2357813‑2357873 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGCATGAACAAGCCATTAAAATTGCTTTGCGCATGCTGGAACAGGGCTTTGATCGTGACCAGGTGCTCGCGGCCACCCAGCTAAGCGAAGCCGATCTGGCAGCGAATAACCACTAATTAACACAGGCCCACAGCCGATCCCCATGGG  >  NC_000913/2357886‑2358032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.