New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	419210 =	115 (1.220)	9 (0.100)	9/236	NT	7.8%	intergenic (+26/‑381)	phoR/brnQ	sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val
	?	NC_000913	419234 =	106 (1.210)					intergenic (+50/‑357)	phoR/brnQ	sensory histidine kinase in two‑component regulatory system with PhoB/branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val

AGGTATATAGCGATAAGAAATCACCAACCAGTATAAAACACTATTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGCATCGA‑‑CTGGCTTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/419364‑419210 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctggcttatTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCC  >  NC_000913/419234‑419380                                                                                                                                                                                                                                                                                                                  AGGTATATAGCGATAAGAAATCACCAACCAGTATAAAACACTATTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGCATCGA‑‑CTG                                                                                                                                                           <  7:426738/149‑1   GTATATAGCGATAAGAAATCACCAACCAGTATAAAACACTATTTCCGTTAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGCATCGA‑‑CTGGC                                                                                                                                                         <  8:76152/149‑1        TAGCGATAAGAAATCACCAACCAGTATAAAACACTATTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGCATCGA‑‑CTGGCTTAT                                                                                                                                                     <  2:398102/148‑1        TAGCGATAAGAAATCACCAACCAGTATAAAACACTATTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGCATCGA‑‑CTGGCTTAT                                                                                                                                                     <  5:55354/148‑1                                            TTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGTCGATG‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACA                                                                                                                >  7:110310/1‑149                                            TTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGTCGATG‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTA                                                                                                                  <  8:110310/147‑1                                                                            ACAAAAAAACACCAATCGTTGTAAACTCTAACGCCCCTATTTTGCCTCCAAAGAAAATAAGCCA‑C‑TCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGC                                                                                <  1:450461/149‑1                                                                                                                                GAAAATAAGCCAGCATCGA‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTC                                                                                           >  2:100026/1‑86                                                                                                                                GAAAATAAGCCAGCATCGA‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTC                                                                                           <  1:100026/86‑1                                                                                                                                   AATAAGCCAGCATCGA‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTG                                          >  6:412292/1‑132                                                                                                                                   AATAAGCCAGCATCGA‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTG                                          <  5:412292/132‑1                                                                                                                                     TAAGCCAGCATCGA‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCTCGGAAATAGTGTTTTA                                                   <  1:390723/121‑1                                                                                                                                     TAAGCCAGCATCGA‑‑CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCTCGGAAATAGTGTTTTA                                                   >  2:390723/1‑121                                                                                                                                                     CTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTT         <  4:232169/149‑1                                                                                                                                                      TGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTT          >  5:126992/1‑147                                                                                                                                                      TGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTATTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTT          >  4:317455/1‑147                                                                                                                                                      TGGCTTATTTACTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCATTTTCACGGAAATAGTGTTTTATACTGGTTGGAGATTTCTTATCGCTATATACCTCTGGTTTT          >  5:189234/1‑147                                                                                                                                                        tCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTA        <  6:412352/146‑1                                                                                                                                                        GCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTA        <  7:10597/147‑1                                                                                                                                                        GCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTA        <  1:97838/147‑1                                                                                                                                                        GCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTT          >  5:314838/1‑145                                                                                                                                                        GCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATAT                      <  2:160985/133‑1                                                                                                                                                        GCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATAT                      >  1:160985/1‑133                                                                                                                                                        GCTTATTTTCTTTGCAGGCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTA        <  6:55354/147‑1                                                                                                                                                            ATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCC  >  4:183101/1‑149                                                                                                                                                             TTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCC  <  2:279053/148‑1                                                                                                                                                                                                                                                                                                                  AGGTATATAGCGATAAGAAATCACCAACCAGTATAAAACACTATTTCCGTGAAAAAGACATGGCTAATCATGCGAACAAAAAATCACCAATCGTTGTAAAATCTAACGCCCGTATTTTGACTGCAAAGAAAATAAGCCAGCATCGA‑‑CTGGCTTAT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/419364‑419210 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ctggcttatTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCC  >  NC_000913/419234‑419380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.