Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	NC_000913	2,868,098	IS5 (+) +4 bp	7.3%	coding (653‑656/1140 nt)	nlpD ←	murein hydrolase activator NlpD

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2868098 =	82 (1.010)	9 (0.110)	9/176	NT	9.5%	coding (656/1140 nt)	nlpD	murein hydrolase activator NlpD
	?	NC_000913	= 3131340	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region
*	?	NC_000913	= 2868101	82 (1.010)	4 (0.050)	4/176	NT	4.4%	coding (653/1140 nt)	nlpD	murein hydrolase activator NlpD
	?	NC_000913	3130146 =	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region
Rejected: Frequency below/above cutoff threshold.

AATTCCACCGTTGCTGTTGCGTCGCAACCGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2868168‑2868098 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAA  <  NC_000913/3131340‑3131254                                                                                                                                                                AATTCCACCGTTGCTGTTGCGTCGCAACCGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCT                                                             <  1:1516593/99‑1   TTCCACCGTTGCTGTTGCGTCGCAACCGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTC                                                           <  2:2211773/99‑1                    CGTCGCAACCGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCAT                                          <  1:1842071/99‑1                      TCGCAACCGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTT                                        >  1:1335928/1‑99                             CGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCT                                 <  1:1652880/99‑1                                       GTATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGA                       <  1:2174124/99‑1                                        TATTCTGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAG                      <  1:464552/99‑1                                             TGAGTCTTCGGGTGAACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGAT                 >  2:1607099/1‑99                                                            ACAGAGTGCTAAGGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAA  >  2:489872/1‑99                                                                                                                                                                AATTCCACCGTTGCTGTTGCGTCGCAACCGACAATTACGTATTCTGAGTCTTCGGGTGAACAGAGTGCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2868168‑2868098 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAATAAGCGGGGAAATTCTTCTCGGCTGACTCAGTCATTTCATTTCTTCATGTTTGAGCCGATTTTTTCTCCCGTAAA  <  NC_000913/3131340‑3131254

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.