New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3440619 =	99 (1.290)	4 (0.050)	4/490	NT	4.8%	coding (409/990 nt)	rpoA	RNA polymerase, alpha subunit
	?	NC_000913	3440886 =	64 (0.860)					coding (142/990 nt)	rpoA	RNA polymerase, alpha subunit

GGGTAACGCACTGCGCCGTATTCTGCTCTCATCGATGCCGGGTTGCGCGGTGACCGAGGTTGAGATTGATGGTGTACTACATGAGTACAGCACCAAAGAAGGCGTTCAGGAAGATATCCTGGAAATCCTGCTCAACCTGAAAGGGCTGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATGAGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3440911‑3440619 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgatgagaGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGGTGTTCGTTAATGTCCGCAGACAGATCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTG  >  NC_000913/3440886‑3441171                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     GGGTAACGCACTGCGCCGTATTCTGCTCTCATCGATGCCGGGTTGCGCGGTGACCGAGGTTGAGATTGATGGTGTACTACATGAGTACAGCACCAAAGAAGGCGTTCAGGAAGATATCCTGGAAATCCTGCTCAACCTGAAAGGGCTGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGAT                                                                                                                                                                                                                                                                                                    >  1:628015/1‑289  GGTAACGCACTGCGCCGTATTCTGCTCTCATCGATGCCGGGTTGCGCGGTGACCGAGGTTGAGATTGATGGTGTACTACATGAGTACAGCACCAAAGAAGGCGTTCAGGAAGATATCCTGGAAATCCTGCTCAACCTGAAAGGGCTGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATG                                                                                                                                                                                                                                                                                                   >  1:3309/1‑289            TGCGCCGTATTCTGCTCTCATCGATGCCGGGTTGCGCGGTGACCGAGGTTGAGATTGATGGTGTACTACATGAGTACAGCACCAAAGAAGGCGTTCAGGAAGATATCCTGGAAATCCTGCTCAACCTGAAAGGGCTGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCAGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTCATCTGCGACCTGCCCGATGAGcacgag                                                                                                                                                                                                                                                                                           >  1:201433/1‑281                                                                                                     GGCGTTCAGGAAGATATCCTGGAAATCCTGCTCAACCTGAAAGGGCTGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGA                                                                                                                                                                                                >  2:185228/1‑289                                                                                                                                                   TGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCAT                                                                                                                                                  >  2:673210/1‑289                                                                                                                                                                TCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTT                                                                                                                                     <  1:185228/289‑1                                                                                                                                                                                                                        CTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATGAGAGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGGTGTTCGTTAATGTCC                                                                              <  1:673210/288‑1                                                                                                                                                                                                                                                                                                     AGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGGTGTTCGTTAATGTCCGCAGACAGATCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTG  >  2:419081/1‑287                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     GGGTAACGCACTGCGCCGTATTCTGCTCTCATCGATGCCGGGTTGCGCGGTGACCGAGGTTGAGATTGATGGTGTACTACATGAGTACAGCACCAAAGAAGGCGTTCAGGAAGATATCCTGGAAATCCTGCTCAACCTGAAAGGGCTGGCGGTGAGAGTTCAGGGCAAAGATGAAGTTATTCTTACCTTGAATAAATCTGGCATTGGCCCTGTGACTGCAGCCGATATCACCCACGACGGTGATGTCGAAATCGTCAAGCCGCAGCACGTGATCTGCCACCTGACCGATGAGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3440911‑3440619 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cgatgagaGCAGAATACGGCGCAGTGCGTTACCCAGAGTATGGCCAAAGCCACGCTCTAAAGGCTCAAGGGTCACCTTGGCGTGCGTCGAACTCACTTGCTCGATATCAACCAGGCGCGGTTTTAGAAACTCTGTCACAGAACCCTGCATTGTGTCCTCTCTTTGGTACTAAGCTTTACTTGGAGTAAAGCTCGACGATCAGGTGTTCGTTAATGTCCGCAGACAGATCAGAACGCTCCGGCTTACGCTTAAACGTACCTTCCATCTTGCCAGCATCAACTTCCAGCCAGGTTG  >  NC_000913/3440886‑3441171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ 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.