New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1045234 =	24 (0.690)	23 (0.660)	20/270	NT	60.5%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
	?	CP009273	= 1973123	6 (0.170)					intergenic (‑669/‑111)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1045376‑1045234 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTC  <  CP009273/1973123‑1972982                                                                                                                                                                                                                                                                                               AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGA                                                                                                                                          <  2:441625/149‑1               GCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATGATACACTAAATCAGTAAATTGGCAGCATCACCTAACGATAATTCAT                                                                                                                                  >  1:299956/1‑143                         TGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCGTCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGA                                                                                                                  <  2:579363/149‑1                         TGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTC‑AAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGct                                                                                                                 >  2:96149/1‑147                                      CACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATA                                                                                                           >  1:264174/1‑143                                             TCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAA                                                                                                    <  1:338636/143‑1                                                          AGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACCCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATA                                                                                 <  2:394053/149‑1                                                                                    GCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATT                                                             >  1:245586/1‑143                                                                                       ACTGGAGAACCTCATACACACCATCATACACTAGATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTG                                                    <  2:345042/149‑1                                                                                            AGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAA                                               <  2:589605/149‑1                                                                                                 gTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGAGGTTA                                                <  1:399450/142‑1                                                                                                  TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAA                                               >  1:270949/1‑143                                                                                                  TCAAAAACACCATAATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAACTAATCAATCACTCCCGGTGCTCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAA                                               >  1:79380/1‑143                                                                                                             acgagACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTC                              <  2:300288/144‑1                                                                                                              TCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCA                             <  2:427750/149‑1                                                                                                              TCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCA                             <  2:551567/149‑1                                                                                                                          TCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACA                       <  1:79900/143‑1                                                                                                                           CAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTT                >  2:5226/1‑149                                                                                                                             GTAAGCTGGCAGCATTACCTAAAGATAATTAATCCAGCTCGCTCGGGGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGA              <  2:432860/149‑1                                                                                                                                     GCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAATTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATT            <  1:374059/143‑1                                                                                                                                       aggATCACCTAAAGATAAATAATCAACCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGTATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGT          <  1:576717/140‑1                                                                                                                                         CATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTC  <  2:296813/149‑1                                                                                                                                         CATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAAAGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTC  >  2:337634/1‑149                                                                                                                                           TCACCTAAAGATAATTAATCACTCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATGGTTGCC      >  1:61097/1‑143                                                                                                                                           TCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCC      >  1:435536/1‑143                                                                                                                                                                                                                                                                                               AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1045376‑1045234 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTC  <  CP009273/1973123‑1972982

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ 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.