New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1978483	0 (0.000)	24 (1.540)	23/308	0.0	100%	intergenic (‑286/+35)	flhD/insB5	DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
	?	NC_000913	= 2070271	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region

CCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAG  >  NC_000913/1978246‑1978694                                                                                                                                                                                                                                              |                                                                                                                                                                                                                    ccccGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGAATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTACTATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTCAACCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCACTAATGCGTGATGCAGATCACACAAAACACTtagactggccccc                                                                                                                                                                                                        >  1:356901‑M1/1‑238 (MQ=255)              ccGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTGTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTAGCTAAGATTGTTCCTAAATCGACGCAACTGTACTCGGCACTACACGCACATACAACGGATGGGGGCTGCGATTTTCAATAAGGCGTGATGCAGATCACACAAAACCCTtagactggccccctgaatctccagac                                                                                                                                                                                           <  1:335695‑M1/251‑27 (MQ=255)                gggAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagaca                                                                                                                                                                                          >  1:9763‑M1/1‑223 (MQ=255)                        ccGGTAAAAAATAAGTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatcgccagacaaccaatatc                                                                                                                                                                                 <  1:17504‑M1/251‑37 (MQ=255)                                                     ttGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatact                                                                                                                                                      >  1:18040‑M1/1‑186 (MQ=255)                                                                                         gTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatg                                                                                                                >  1:4362‑M1/1‑150 (MQ=255)                                                                                                         cAAATAGAAATTGGTCTTTACACGTATCTAAGATTGTTCCTAAATCAACGCAACTGTAATCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAAGGCGTGAGGCAGATCACACAAAACACCtagactggccctctgaatctccagacaaccaatatcacttaaataagt                                                                                                                                                                     <  1:49820‑M1/182‑49 (MQ=255)                                                                                                              aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGAGGCAGATCACACAAAACACTtagactgtccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttgtactagtcattggagaacagatgattgatgtcttagggccggagaaacgc                                                                                            <  1:166318‑M1/250‑122 (MQ=255)                                                                                                                               cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAACCACTtagactggccccttgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtca                                                                                                                                     <  1:191003‑M1/192‑81 (MQ=255)                                                                                                                               cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACCCGTCACTACACGCACATACAACGGAGGGGGGCTGCCATTGTCAATAAGGCGTGATGCAGATCTCACAAAACACTtagactggccccctgaatctgcagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagac                                                                                                                                           <  1:206886‑M1/186‑75 (MQ=255)                                                                                                                                    cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttaggtccggagaaacgcagacggcgtacc                                                                                >  1:288061‑M1/1‑107 (MQ=255)                                                                                                                                    cTAAGATTTTTCCTAAAGCGACGCAACTGGACGCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctcc                                                                                                                                                                                               <  1:121876‑M1/129‑23 (MQ=255)                                                                                                                                                                gTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattgtagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttg                                           <  1:306482‑M1/249‑171 (MQ=255)                                                                                                                                                                      gTCACTACACGCCCATACAACGGAGGGGGGCTGCGATTTTCCATAATGCGTGCTGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttactactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgta                                                                                  >  1:199805‑M1/1‑73 (MQ=255)                                                                                                                                                                         ggcagcgaacgggacaacggaggggggCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagttcgcaattgttcagcagagctttgaaccggggatg                                <  1:121713‑M1/238‑182 (MQ=255)                                                                                                                                                                            acacGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccatacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttgaaccggggatgacn                             <  1:215176‑M1/251‑185 (MQ=255)                                                                                                                                                                                       cAACGGAGGGGGGCTGCGATTTTCAATAATGCATGATGCAGATCACACAAAACACTtcgactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccgcacaggaaaagatcgcaattgttcagcagcgctttgaaccggggatgacggtctccctcgt                  >  1:117266‑M1/1‑56 (MQ=255)                                                                                                                                                                                               gggggCTGCGATTTTAAATAATGCGTGCTGCTGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactcgtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcg                                                                >  1:280524‑M1/1‑48 (MQ=255)                                                                                                                                                                                                       cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttgaaccggggatgacggtctccctcgttgcccggcaacatggt  >  1:273959‑M1/1‑40 (MQ=255)                                                                                                                                                                                                       cGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcagagctttgaaccggggatgacggtctccctcgttgcccggc          <  1:256388‑M1/243‑204 (MQ=255)                                                                                                                                                                                                            tnNAATAATNNGTGATGCAGATCACTCAAAACACTtagactggccccctgaatctccagacaaacaatatcacttaaataagtgatcgtcttaatacta                                                                                                                                                     <  2:21126‑M1/99‑65 (MQ=255)                                                                                                                                                                                                              cAATAATGCGTGATGCAGATCACACAAAACACTtagactggccccctgaatctcaagacaaccaatatcaattaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggcc                                                                                                      >  1:47514‑M1/1‑33 (MQ=255)                                                                                                                                                                                                                              aGATCACACAAAACACTtagactggccccctgaatctccagccaaccaatatcacttaaataagagctagccttaatactagtttttagactagtcattggagaacagctgattgatgtcttagggccggagaaacgcagacggagtaccacacaggaaaagatcgcaattgttcagcagagctttgaaccggggatgacggtctccctcgttgcccgg           >  1:325208‑M1/1‑17 (MQ=255)                                                                                                                                                                                                                                  cacacaAAACACTtagactggccccctgaatctccagacaaccaatatcacttaaataagtgatagtcttaatactagtttttagactagtcattggagaacagatgattgatgtcttagggccggagaaacgcagacggcgtaccacacaggaaaagatcgcaattgttcagcag                                                  >  1:316462‑M1/1‑13 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                    CCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTAGCATTAGAATAGTTGCGATAAGCTGCAATAAGCAGAACCACCTTTTTGGTTTAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAG  >  NC_000913/1978246‑1978694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ 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.