New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2288919 =	NA (NA)	18 (0.200)	16/598	4.0	16.4%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	3658971 =	92 (1.010)					intergenic (+78/‑21)	gadE/gadF	DNA‑binding transcriptional activator GadE/small regulatory RNA GadF
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AGCGACAGTTCGGCTTCGTGAAAGCCAGATACAAGGGGTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2289198‑2288919 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTCTCCTCGCGCGCAATTTAAAGAACCGTTATTTCTCAAGAATTTTCAGGGACTAAAATGAACAGAAGAAGAAAGCTGTTAATACCGTTGTTAT  >  NC_000913/3658971‑3659268                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    AGCGACAGTTCGGCTTCGTGAAAGCCAGATACAAGGGGTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACG                                                                                                                                                                                                                                                                                        <  1:9193/300‑1                       AGCCAGATACAAGGGGTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGT                                                                                                                                                                                                                                                                  <  1:613009/300‑1                                                                                         GTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGANAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTANAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTT                                                                                                                                                                                                >  2:727616/1‑300                                                                                                             TACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCA                                                                                                                                                                            <  1:152826/300‑1                                                                                                                GTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACNTGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGT                                                                                                                                                                         <  1:559915/300‑1                                                                                                                    GTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGAT                                                                                                                                                                     >  1:486343/1‑300                                                                                                                       ggatAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGTAGAAAAAATCGGCTCAAACATTAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCAC                                                                                                                                                                  <  2:34189/296‑1                                                                                                                                                                  AAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCC                                                                                                                       >  2:435763/1‑300                                                                                                                                                                         GGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCAGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCACTGGTATGTGTATCCAACAGTAGAACCCTTAGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGTTGGTt                                                                                                                >  2:118157/1‑299                                                                                                                                                                              AAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAANCGACTTTATTCCCCTGGTATGTGTATNCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCAACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAA                                                                                                           >  2:523190/1‑300                                                                                                                                                                              AAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAA                                                                                                           >  1:769242/1‑300                                                                                                                                                                                                                 ATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTCTCCTCGCGCGCAATTTAAAGA                                                                        <  1:405351/300‑1                                                                                                                                                                                                                    GGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTCctgtctcttatacacatctcgcag                                                                     <  1:32993/300‑25                                                                                                                                                                                                                                                    CAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTCTCCTCGCGCGCAATTTAAAGAACCGTTATTTCTCAAGAATTTTCAGGGACTAAAAT                                     <  1:502953/300‑1                                                                                                                                                                                                                                                             AGAATTTCTCCTCTTATTCGCACCTTCCCTAAAGTAGATGCTAAACCTACTCTATTCCCCTGGTATGTATATCCACCAGTAGAACCCTTCTTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCGGTAAATCCCTCATATCTCTCCTCGCGCGCAATTTAAAGAACCGTTATTGCTCAAGAATTGTCAGGGACTAAAGGGAACAGAAG                            <  2:273009/300‑1                                                                                                                                                                                                                                                                  TTCCCCGCTTATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTCTCCTCGCGCGCAATTTAAAGAACCGTTATTTCTCAAGAATTTTCAGGGACTAAAATGAACAGAAGAAGAA                       <  1:190950/300‑1                                                                                                                                                                                                                                                                           TATTCGCACCTTCCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTATGTAAATCCCCCATATCTCTACTCGCGCGCAATTTCAAGAACCGTTATTTCTCAAGAATTTTCAGGGACTAAAACGAACAGACGAAGAAAGCCGTTAc              >  2:62468/1‑299                                                                                                                                                                                                                                                                                       CCCTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGNACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCATGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTATCCTCGCGCGCAATTTAAAGAACCGTTATTTCTCAANAATTTTCAGGGACTAAAATGAACAGAAGAAGAAAGCTGTTAATACCGTTGTTAT  >  2:715339/1‑300                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    AGCGACAGTTCGGCTTCGTGAAAGCCAGATACAAGGGGTTGCTGAAAAACGATAACCAACTGGCGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2289198‑2288919 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAAGGAGAGGCTAAAACGACTTTATTCCCCTGGTATGTGTATCCACCAGTAGAACCCTTCGTTGCCCGAATGCTGGCAGGAACTGTTGGCAGAACGGCAACATTTTTTTTGTCGTTGACCTCACCATGTCGATCACTGTGCCTGTATCCCACCTTACTGGCTGACAACCCCACTATGCCGCTGGTCTGTAAATCCCTCATATCTCTCCTCGCGCGCAATTTAAAGAACCGTTATTTCTCAAGAATTTTCAGGGACTAAAATGAACAGAAGAAGAAAGCTGTTAATACCGTTGTTAT  >  NC_000913/3658971‑3659268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 25 ≤ 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.