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.

CTCGGTTGTGCTTGCTGTTGGTACCGTTACAGGCGCTGTGACCGTGGTCGCAGTTGGCTTGTTGTTCGGCAACATTTTGTTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2868019‑2868101 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTT  >  NC_000913/3130146‑3130233                                                                                                                                                                             CTCGGTTGTGCTTGCTGTTGGTACCGTTACAGGCGCTGTGACCGTGGTCGCAGTTGGCTTGTTGTTCGGCAACATTTTGTTAGGGAAGGTGCGAACAAG                                                                          <  2:1233525/99‑1                           TTACAGGCGCTGTGACCGTGGTCGCAGTTGGCTTGTTGTTCGGCAACATTTTGTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCA                                                <  2:1918789/99‑1                               AGGCGCTGTGACCGTGGTCGCAGTTGGCTTGTTGTTCGGCAACATTTTGTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTG                                            >  2:2154789/1‑99                                                                         CATTTTGTTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTT  <  1:518868/99‑1                                                                                                                                                                             CTCGGTTGTGCTTGCTGTTGGTACCGTTACAGGCGCTGTGACCGTGGTCGCAGTTGGCTTGTTGTTCGGCAACATTTTGTTAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2868019‑2868101 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTT  >  NC_000913/3130146‑3130233

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ 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.