New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3648146	114 (1.090)	11 (0.130)	9/468	5.4	10.0%	intergenic (+2/‑148)	agrA/agrB	small RNA AgrA/small regulatory RNA AgrB
	?	NC_000913	3648378 =	106 (1.270)					intergenic (+3/‑150)	agrB/arsR	small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

AACTCTCTCACTCCGGCCAGAGCATCAGTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3647873‑3648146 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagagccaccaactcagggctggaaagtaaaaaaccgacgcaaagtcggtttttttacGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGGAGCGCAATATGTCATTTCTGTTACCCATCCAATTGTTCAAAATTCTTGCTGATGAAACCCGTCTGGGCATCGTTTTAC  >  NC_000913/3648378‑3648597                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                AACTCTCTCACTCCGGCCAGAGCATCAGTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATTCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAA                                                                                                                                                                                                     <  2:439264/299‑1                                                                             CGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCGGATTCAGACCTCATTTCATATGAAga                                                                                                                                                                                               >  1:506033/1‑227                                                                                                                     ATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGG                                                                                <  1:579989/300‑1                                                                                                                     ATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCA                                                                                  >  2:579989/1‑298                                                                                                                             GTACATGTAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGCCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCCAAATTCACACCTATTACCTTCCTATGCACTTACACATTCGTTAAGTCGTATATGTTTTTGACTTATCCGCTTCGAAGGGAGAAACTACCTGCAACAATCAGGAGCGta                                                                          >  2:586885/1‑296                                                                                                                             GTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTACCTTCACATGAATAGCCAACTCCAAATTCACAC                                                                                                                                                                            >  1:494815/1‑200                                                                                                                                   gccGGTTATAAAAACAGCGCGTCCTTGCAATGGTTTCAGTATGTTAGTAGTATTGATGTGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTACTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGGAGCGCAATATGTC                                                                   <  2:506033/296‑1                                                                                                                                                        TCCTTGCAATATTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGGAGCGCAATATGTCATTTCTGTTACCCATCCAATTG                                             <  2:494815/300‑1                                                                                                                                                                         GTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACATCCTGATTCAGACCcaacttcacatga                                                                                                                                                                                                  >  2:812142/1‑121                                                                                                                                                                                                          CTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGGAGCGCAATATGTCATTTCTGTTACCCATCCAATTGTTCAAAATTCTTGCTGATGAAACCCGTCTGGGCATCGTTTTAC  <  1:729024/293‑1                                                                                                                                                                                                          CTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTACGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGGAGCGCAATATGTAATTTCTGTTCCCCACCCAATTGTTCAAAATTCTTGCTGATGAAACCCGTCTGGGCATTGTTTTcc  >  2:729024/1‑291                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                AACTCTCTCACTCCGGCCAGAGCATCAGTTAACGGCACCACCCGTACTTCTGACCAGGACTTTGAAAGCGTTTATGCGCATTGCCAGAGTGAAAATGCCTCAGAGCTAACTGGATAATCATACAGTACATGCAGGTTATAAAACCAGCACGTCCTTGCAATAGTTTCAGTATGGTATTAGCATTGATGCGTTAGATGATGGCTATCTCACTCCAGTCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAAACCGACGCAAAGTCGGTTTTTTTAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/3647873‑3648146 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagagccaccaactcagggctggaaagtaaaaaaccgacgcaaagtcggtttttttacGTCCTGATTCAGACCTCCTTTCAAATGAATAGCCAACTCAAAATTCACACCTATTACCTTCCTCTGCACTTACACATTCGTTAAGTCATATATGTTTTTGACTTATCCGCTTCGAAGAGAGACACTACCTGCAACAATCAGGAGCGCAATATGTCATTTCTGTTACCCATCCAATTGTTCAAAATTCTTGCTGATGAAACCCGTCTGGGCATCGTTTTAC  >  NC_000913/3648378‑3648597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ 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.