Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	KT2440	4,263,135	Δ15 bp	6.8%	intergenic (‑190/‑357)	pcaK_3 ← / → mrdA_1	4‑hydroxybenzoate transporter PcaK/Peptidoglycan D,D‑transpeptidase MrdA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	KT2440	= 4263134	53 (1.250)	4 (0.090)	4/234	NT	6.8%	intergenic (‑189/‑372)	pcaK_3/mrdA_1	4‑hydroxybenzoate transporter PcaK/Peptidoglycan D,D‑transpeptidase MrdA
	?	KT2440	4263150 =	56 (1.320)					intergenic (‑205/‑356)	pcaK_3/mrdA_1	4‑hydroxybenzoate transporter PcaK/Peptidoglycan D,D‑transpeptidase MrdA

CAACGGGAGGAACCCTGACGGTTCAGTGCCGCTGGATAGCCATTCATGACTGGACCCTTTTTGTAATTGTTATCGCATACGGCAGGAGGGCTCCGGCCGTTGTCAGGCGCTAATCAACCAGATAATGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  KT2440/4263006‑4263134 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ACGAAACCACTGCCTAACTATCAGGCGCGACCAATTTCAGTTCATTGCCAGTAAAAATCATATTTTTTATAAATAAATTCAATAGTTTATAAATTCACAACCAACGAAAACTGATGTTCGGTTACC  >  KT2440/4263150‑4263275                                                                                                                                                                                                                                                                 CAACGGGAGGAACCATGACGGTTCTGTGCCTCTGGATAGCCATTCATGACTGGACCCTTTTTGTAATTGTTATCGCATACGGCAGGAGGGCTCCGGCGGTTGTCAGGCGCTAATCAACCAGATAATGGAACGAAA                                                                                                                          <  2:126429/135‑1                                                                                              CGGCCGTTGTCAGGCGCTAATCAACCAGATAATGGAACGAAACCACTGCCTAACTATCAG                                                                                                        >  7:81673/1‑60                                                                                              CGGCCGTTGTCAGGCGCTAATCAACCAGATAATGGAACGAAACCACTGCCTAACTATCAG                                                                                                        <  8:81673/60‑1                                                                                                                         GATAATGGAACGAAACCACTGCCTAACTATCAGGCGCGAGCATTTTCAGTTCATTGCCAGTAAAAATAATATTTTATATAAATAAATTCTATAGTTTATAAATTCACAAGCAACCAAAAATTTTGTTCGGTTACC  <  1:212370/135‑1                                                                                                                                                                                                                                                                 CAACGGGAGGAACCCTGACGGTTCAGTGCCGCTGGATAGCCATTCATGACTGGACCCTTTTTGTAATTGTTATCGCATACGGCAGGAGGGCTCCGGCCGTTGTCAGGCGCTAATCAACCAGATAATGGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  KT2440/4263006‑4263134 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ACGAAACCACTGCCTAACTATCAGGCGCGACCAATTTCAGTTCATTGCCAGTAAAAATCATATTTTTTATAAATAAATTCAATAGTTTATAAATTCACAACCAACGAAAACTGATGTTCGGTTACC  >  KT2440/4263150‑4263275

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ 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.