New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1045234 =	98 (1.400)	49 (0.700)	36/276	NT	45.2%	intergenic (‑34/‑55)	gfcA/insA	O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA
	?	CP009273	= 1973123	21 (0.300)					intergenic (‑669/‑111)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

AGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1045380‑1045234 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTT  <  CP009273/1973123‑1972979                                                                                                                                                                                                                                                                                                      AGATAGCGCTGATGTCCGGCAGTGCTTTTTCCTTTATGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTGAATCAGTAAGTTGGCAGCATAACCTA                                                                                                                                                 >  2:1111198/1‑149    TAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCCCAAAAACACCATCATACACTAAACCAGCAAGTCGGCAGCACCCCCTAAAG                                                                                                                                              >  2:476504/1‑149     AGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAAAAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATCCACTAAATCAGTAAGTTGGCAGCATCACCTAAAGA                                                                                                                                             >  2:598854/1‑149      GCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAACGAT                                                                                                                                            >  1:315359/1‑149          tggTGTCCGGCAGTGCTTTTGCCGTTGCGCCCCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATT                                                                                                                                        <  2:1195153/146‑1             TGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGCAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAAT                                                                                                                                     <  1:1212249/149‑1             TGTCCGGCAGTGCTTTTGCCGTTACCCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAAT                                                                                                                                     <  1:951599/149‑1                 CGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAAT                                                                                                                                 >  1:492011/1‑149                       TGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCCTCACCTAAAGATAATTAATCAATCACTCC                                                                                                                           >  1:362492/1‑149                                CGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCA                                                                                                                  <  1:482864/149‑1                                   TACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATAT                                                                                                               >  1:1155522/1‑149                                      GCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAAT                                                                                                            >  1:38594/1‑149                                        ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTT                                                                                                          >  2:345171/1‑149                                         CCACCCCGTCAGTAGCTGAACAGGTGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCTTGAGCTAAAGATAATTAATTAATCACTCGCGCTGATCATATAATTTt                                                                                                         >  1:199408/1‑148                                         CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTcc                                                                                                         >  2:674942/1‑147                                         CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGCGATCATATAAATTC                                                                                                         >  2:404324/1‑149                                         CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGAGATCATATAATTTC                                                                                                         >  1:1193771/1‑149                                         CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATACTACACTAAAGCAGTATGCTGATATCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTC                                                                                                         >  1:544245/1‑149                                            CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCCCCTAAAGATAATTAATCAATCACTCCCGGCGATCATATAATTTCAAA                                                                                                      >  2:666254/1‑149                                            CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAca                                                                                                      >  2:328222/1‑147                                            CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAA                                                                                                      <  1:1200899/149‑1                                                GTCAGTAGGTGAACAGGAGGGACAGCTGATAGAAGCAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAATTCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTTTTCATATAATTTCAAATGTA                                                                                                  <  2:973977/149‑1                                                GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTA                                                                                                  <  1:629054/149‑1                                                GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATGTCAAATGTA                                                                                                  <  1:263681/149‑1                                                 TCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAA                                                                                                 >  1:582638/1‑149                                                           AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAA                                                                                       >  2:734519/1‑149                                                                     ACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACT                                                                             >  1:64814/1‑149                                                                     ACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACT                                                                             >  1:731907/1‑149                                                                          TGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTC                                                                        <  1:742977/149‑1                                                                               GAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCGCCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGAGTCTCCGC                                                                   >  1:99118/1‑149                                                                               GAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGC                                                                   <  1:61933/149‑1                                                                                AAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCA                                                                  >  1:721377/1‑149                                                                                   CAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTA                                                               >  1:1155831/1‑149                                                                                   CAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTA                                                               >  1:189973/1‑149                                                                                                                 ATCATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTC                                 >  1:115139/1‑149                                                                                                                    ATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATCTGTAAAACATTTCATT                              >  1:42887/1‑149                                                                                                                    ATACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATT                              >  1:861927/1‑149                                                                                                                     TACACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTA                             <  2:38594/149‑1                                                                                                                     TACACTAAATCAGTAAGTTGGCAGAATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAACTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTA                             <  2:414392/149‑1                                                                                                                       CACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAAC                           <  2:789107/149‑1                                                                                                                        ACTAGAGCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACA                          <  2:656240/149‑1                                                                                                                        ACTAAATCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACA                          >  1:193700/1‑149                                                                                                                              TCAGTAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGT                    <  1:345171/149‑1                                                                                                                                  TAAGTTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTCAAACATTCCATTAACActcacatgac                >  2:253414/1‑139                                                                                                                                      TTGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTT            >  2:864825/1‑149                                                                                                                                       TGGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTG           >  1:545292/1‑149                                                                                                                                        GGCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGATGC          >  1:662061/1‑149                                                                                                                                         GCAGCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTTAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCC         >  1:35145/1‑149                                                                                                                                            GCATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAACATAGTGTACTGATTCTCCGCATTAAACAAGTAGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTT      >  2:243939/1‑149                                                                                                                                             CATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTC     >  2:766228/1‑149                                                                                                                                              attACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATCTATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCT    <  2:755790/146‑1                                                                                                                                              ATCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCT    <  1:521892/149‑1                                                                                                                                               TCACCTAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTT   >  1:615706/1‑149                                                                                                                                                CACTTAAAGATAATTAATCAAACACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTT  <  1:7915/149‑1                                                                                                                                                CACCTAAAGATAATTAATCAATCACCCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTT  <  1:7467/149‑1                                                                                                                                                                                                                                                                                                      AGATAGCGCTGATGTCCGGCAGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGAACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1045380‑1045234 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TAAAGATAATTAATCAATCACTCCCGGTGATCATATAATTTCAAATGTAATTATAAGAAAATAGTGTACTGATTCTCCGCATTAAACAAGTGGTTAATATATGTAAAACATTTCATTAACATTAAGTTGATTGTTGCCTTTCTTT  <  CP009273/1973123‑1972979

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.