New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1045234 =	27 (1.010)	23 (0.860)	18/276	NT	52.9%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
	?	CP009273	= 1973123	14 (0.530)					intergenic (‑669/‑111)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1045376‑1045234 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTT  <  CP009273/1973123‑1972980                                                                                                                                                                                                                                                                                                 AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCAACACCTAAAGA                                                                                                                                            >  2:111821/1‑149         TGTCCGGCAGTGCTTGTGCCGCTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAAT                                                                                                                                    <  2:355690/149‑1         TGTCCGGAAGTGCTGTGGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAAT                                                                                                                                    <  2:355652/149‑1                          GCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGAT                                                                                                                   <  1:372280/149‑1                          GCCGGTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGAT                                                                                                                   <  1:256818/149‑1                           CCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATACTTAATCACTCACTCCCGGTAATC                                                                                                                  >  1:268296/1‑149                           CCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATC                                                                                                                  >  1:180898/1‑149                                    ACCACCCCGTCACAAGGTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATAAAATTT                                                                                                         >  2:172112/1‑149                                        CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAA                                                                                                     <  1:37099/149‑1                                               AGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATT                                                                                              <  1:53689/149‑1                                                 TAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTAT                                                                                            >  1:67685/1‑149                                                          AGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATGAGAAAATA                                                                                   >  2:196769/1‑149                                                          AGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATA                                                                                   >  2:354294/1‑149                                                                          AGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATCGTGTACTGATTCTCCG                                                                   <  1:229031/149‑1                                                                              ACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATT                                                               <  2:67685/149‑1                                                                                                 CTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATAT                                            <  1:111821/149‑1                                                                                                  TCAAAAACACCATGATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATACTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATG                                           >  1:331357/1‑149                                                                                                    AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTA                                         >  2:112265/1‑149                                                                                                          ACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACAT                                   <  1:388490/149‑1                                                                                                                    ACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACA                         >  1:416021/1‑149                                                                                                                    ACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACA                         >  1:19534/1‑149                                                                                                                              TAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGTTTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGAT               >  1:461392/1‑149                                                                                                                                          ATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCT   <  1:454686/149‑1                                                                                                                                           TCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAACCATTTCATTAACATTAAGTTGATTGTTGCCTTTCTT  >  1:117812/1‑149                                                                                                                                           TCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTT  >  1:291385/1‑149                                                                                                                                                                                                                                                                                                 AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1045376‑1045234 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTT  <  CP009273/1973123‑1972980

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ 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.