New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1972748 =	0 (0.000)	52 (1.160)	33/294	0.4	100%	intergenic (‑294/‑486)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
	?	CP009273	= 2283592	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region

TATTTACGGTGAGTTATTTTGACTGTGCGCAACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAg‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1972890‑1972748 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGC  <  CP009273/2283592‑2283444                                                                                                                                                                                                                                                                                                      TATTTACGGTGATTTATTTTGGCTGTGCGCTACATCCCATTTCGATTATACCTGTTTCATTTTTGCTTGTGAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGG                                                                                                                                                 <  2:80298/149‑1       CGGTTAATTATTTTGACTGTGCCCACCAAACCACTTCGATTATTCCTGTTTCATTTTTCCCTTCTAGCGGAGCGAAAAACTTTTTAACAGAGTCAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAA                                                                                                                                           <  2:613632/149‑1       CGGTGAGTTATTTTGACTGTGCGCAACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAA                                                                                                                                           <  2:407117/149‑1       CGGTGAGTTATTTTGACTGTGCGCAACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAA                                                                                                                                           <  1:426479/149‑1              ttatgtgtACTGTGCGCAACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCC                                                                                                                                    >  2:527586/9‑149                        TGTGCGCAACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAG                                                                                                                          >  2:75306/1‑149                           GCGCCACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGAAAAGAAAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATC                                                                                                                       <  2:23128/149‑1                                ACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTT                                                                                                                  <  1:488358/149‑1                                 CATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                                                                                 <  1:655751/149‑1                                             ATTATTCCTGTTTCATTTTTTCTTTTTATCTTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGTTCATGTTTGTCCTCTGGAGC                                                                                                     >  2:546333/1‑149                                               TATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTCACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCA                                                                                                   <  2:453133/149‑1                                                ATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTCTACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATTTGAGATCATGTTTGTCATCTGGAGCCAT                                                                                                  <  1:443815/149‑1                                                     TGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAAC                                                                                             >  1:458050/1‑149                                                      tTTTCATTTTTGCTGGCTACCGTCGCGCAAAACTTTCTAACAGAGTGAAATCAATCCCAAACAAAAGTATGACTTATATATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGTTCATGTTTGTCATCTGGAGCCATAGAACA                                                                                            <  1:517620/148‑1                                                       TTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAAAAAGTCCCTGATATGAGATCATGTTTGTCTTCTGGAGCCATAGAACAa                                                                                           >  2:426094/1‑148                                                        TTCATTTTTGCTTGCTAGCGGACCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGG                                                                                          <  1:146204/149‑1                                                         TCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAAAAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCAATAGAACAGGG                                                                                         >  1:436920/1‑149                                                          CATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGT                                                                                        >  1:117021/1‑149                                                                  CTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGGATGACTTATACATTTATGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATATGGAGCCATAGAACAGGGTTCATCATG                                                                                >  1:512562/1‑149                                                                   TTGCTAGCGTAGCGAAAACCTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                               <  2:436860/149‑1                                                                   TTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATAGACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                               <  2:339561/149‑1                                                                   TTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                               <  1:545015/149‑1                                                                     gccAGCGTAGCGAAAAACTTGTTAACAGTATAAAATACACACAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGT                                                                             <  2:48149/146‑1                                                                       TAGCGTAGCGAAAAACTTTTTAACAGATTCAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCA                                                                           >  1:518872/1‑149                                                                            TAGCGAAAAACTTTTTAACTGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAAC                                                                      <  1:198975/149‑1                                                                               CGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTATCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCAACAACTTA                                                                   >  2:73954/1‑149                                                                                      CTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGC                                                            >  1:271957/1‑149                                                                                                GATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAA                                                  <  2:346955/149‑1                                                                                                       ATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGCACGAGGTTCATCATGAGTCATCAAATTACCTTCGCCGACAGAGAATTCAGCA                                           >  1:124459/1‑149                                                                                                             CCAAAACAAAATTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCCACAACTCATTTGCTCCGACAGTGAATTCAGCAGTAAGC                                     <  2:709578/149‑1                                                                                                             CCAAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGC                                     >  2:691202/1‑149                                                                                                               AAAACAAAAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGC                                   <  1:183641/149‑1                                                                                                                  ACAATAGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGT                                <  1:477085/149‑1                                                                                                                       AGTATGACTTATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGAC                           >  1:28414/1‑149                                                                                                                             cCTTCTACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGGTATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGTTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCATAAA                     <  2:271957/148‑1                                                                                                                                TATACATTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGA                  <  1:694937/149‑1                                                                                                                                TATACATATATGTAAAGGAAGGTGCGAACAAGACCCTGATATGAGATCATGTTTGTCCTCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGA                  <  1:427359/149‑1                                                                                                                                      TTTATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAAAATATGGTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTT            >  1:727705/1‑149                                                                                                                                         ATGTTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCCGAAACGAGATTTTCTT         >  2:70710/1‑149                                                                                                                                            TTAAGGACGGTGCGCACACGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAAGTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTC      <  1:291230/149‑1                                                                                                                                             TAAGGAAGGTGCGAACACGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGATCAGGGTTCATCATGAGTCATCAACTTACCTTCGCCAACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC     >  2:543729/1‑149                                                                                                                                             TAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCGGACCAGGAAAGGGATTTTCTTGTCC     >  1:382242/1‑149                                                                                                                                             TAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC     <  2:350366/149‑1                                                                                                                                             TAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCAAAAAGTTAACTGTTCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC     >  1:537260/1‑149                                                                                                                                              AAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGCGATTTTCTTGTCCC    >  2:45641/1‑149                                                                                                                                              AAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGCTTTTCTTGTCCC    >  1:172455/1‑149                                                                                                                                              AAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC    >  1:118473/1‑149                                                                                                                                              AAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCC    <  2:696571/149‑1                                                                                                                                               AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGATCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGGATTCAGCAGTAAGCGCCGTGCAACCAGAAAAGAGATTTTGTTGTCCCG   >  2:37169/1‑149                                                                                                                                               AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG   >  1:556341/1‑149                                                                                                                                               AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG   >  2:471330/1‑149                                                                                                                                               AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGGTTGTCATCTGGAGCCATAGAACAGGGGTGATCATGAGGCATCAACTGGCCTTCGCCGCCAGTGAATTCAGCAGGAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTCTCCCG   >  2:56416/1‑149                                                                                                                                                GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGGTTTTCTTGTCCCGC  >  1:272467/1‑149                                                                                                                                                                                                                                                                                                      TATTTACGGTGAGTTATTTTGACTGTGCGCAACATCCCATTTCGATTATTCCTGTTTCATTTTTGCTTGCTAGCGTAGCGAAAAACTTTTTAACAGATTGAAATACACCCAAAACAAAAGTATGACTTATACATTTATGTTAAg‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/1972890‑1972748 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCGC  <  CP009273/2283592‑2283444

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.