New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	4972749 =	71 (1.150)	3 (0.050)	3/330	NT	4.6%	coding (799/1566 nt)	flgL	Flagellar hook‑associated protein FlgL
	?	AE015451	4972820 =	56 (0.940)					coding (728/1566 nt)	flgL	Flagellar hook‑associated protein FlgL
Rejected: Frequency below/above cutoff threshold.

CACCAACAACAGCCGCACCCAGTCGAGCCTGGTAGCACCGTCGCCGGATGACGGCAAGGTATTGCTGTCTGGCGGCCTGTTGACCTCGGCCACCACCTACGGCAATCAGTTTGCCGCTGGTCAGCCGTATTCTGTCACCTTCACCAGTGCCACCGAGTACAGCGTGAGGGATGCCGCCGGCAATGACATCACCAATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAGGCGGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/4972990‑4972749 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggcggcaTCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCATCCGGCGACGGTGCTACCAGGCTCGACTGGGTGCGGCTGTTGTTGGTGGCCTGGTCGAAAATGCTGTAGCCGGTGTCGTTGGTCGCCAGGCGCAAGGTGTCGGACACCTG  >  AE015451/4972820‑4973052                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             CACCAACAACAGCCGCACCCAGTCGAGCCTGGTAGCACCGTCGCCGGATGACGGCAAGGTATTGCTGTCTGGCGGCCTGTTGACCTCGGCCACCACCTACGGCAATCAGTTTGCCGCTGGTCAGCCGTATTCTGTCACCTTCACCAGTGCCACCGAGTACAGCGTGAGGGATGCCGCCGGCAATGACATCACCAATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAG                                                                                                                                                                                                                                                 >  1:657178/1‑236                           GCCTGGTAGCACCGTCGCCGGATGACGGCAAGGTATTGCTGTCTGGCGGCCTGTTGACCTCGGCCACCACCTACGGCAATCAGTTTGCCGCTGGTCAGCCGTATTCTGTCACCTTCACCAGTGCCACCGAGTACAGCGTGAGGGATGCCGCCGGCAATGACATCACCAATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAGGC                                                                                                                                                                                                                                               <  1:896360/212‑1                                                                                                                                                                                                 CAATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAGGCGGCATCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCACCCGGCGACGGTGCTACCAGGCTC                                                                                        <  1:249133/197‑1                                                                                                                                                                                                  AATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAGGCGGCATCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCATCCGGCGACGGTGCTACCAGGCTCGACTGGGTGCGG                                                                            >  1:528742/1‑208                                                                                                                                                                                                  AATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAGGCGGCATCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCATCCGGCGACGGTGCTACCAGGCTCGACTGGGTGCGG                                                                            <  2:528741/208‑1                                                                                                                                                                                                                                                 CATCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCATCCGGCGACGGTGCTACCAGGCTCGACTGGGTGCGGCTGTTGTTGGTGGCCTGGTCGAAAATGCTGTAGCCGGTGTCGTTGGTCGCCAGGCGCAAGGTGTCGGACACCTG  >  1:477212/1‑235                                                                                                                                                                                                                                                 CATCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCATCCGGCGACGGTGCTACCAGGCTCGACTGGGTGCGGCTGTTGTTGGTGGCCTGGTCGAAAATGCTGTAGCCGGTGTCGTTGGTCGCCAGGC                     <  1:824288/216‑1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             CACCAACAACAGCCGCACCCAGTCGAGCCTGGTAGCACCGTCGCCGGATGACGGCAAGGTATTGCTGTCTGGCGGCCTGTTGACCTCGGCCACCACCTACGGCAATCAGTTTGCCGCTGGTCAGCCGTATTCTGTCACCTTCACCAGTGCCACCGAGTACAGCGTGAGGGATGCCGCCGGCAATGACATCACCAATGAAACCGCCGGCAAGGGCAAGTTCGACGTCAATACCGAAGGCGGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  AE015451/4972990‑4972749 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ggcggcaTCCCTCACGCTGTACTCGGTGGCACTGGTGAAGGTGACAGAATACGGCTGACCAGCGGCAAACTGATTGCCGTAGGTGGTGGCCGAGGTCAACAGGCCGCCAGACAGCAATACCTTGCCGTCATCCGGCGACGGTGCTACCAGGCTCGACTGGGTGCGGCTGTTGTTGGTGGCCTGGTCGAAAATGCTGTAGCCGGTGTCGTTGGTCGCCAGGCGCAAGGTGTCGGACACCTG  >  AE015451/4972820‑4973052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ 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.