New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 2406863	2 (0.040)	46 (1.030)	37/274	NT	95.9%	intergenic (‑224/‑696)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
	?	NC_000913	2996360 =	NA (NA)					intergenic (‑2/+10)	ygeO/insD1	pseudogene, orgA family, part of T3SS PAI ETT2 remnant/IS2 transposase TnpB

TGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2406715‑2406863 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  >  NC_000913/2996360‑2996506                                                                                                                                                                                                                                                                                                          TGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACT                                                                                                                                                     <  2:27319/149‑1       TCCCTCGCAGTTTCATCCGGACCCCGGACGAAAGTAAAATTGCATATGAATTGAAATAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTT                                                                                                                                               <  2:614219/149‑1          cgGGCAGTTTCATCCGGAACCCGGCCGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCC                                                                                                                                            <  1:723/147‑1             GCAGTTTCATCCGGAACCGGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCT                                                                                                                                         <  1:37205/149‑1             GCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCT                                                                                                                                         <  2:802489/149‑1                  TTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATT                                                                                                                                    >  1:689697/1‑149                      TCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTACAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATTTCTTCAGGGATCGCATATCTATTAAGTTACTGGTTTTGCCCCTATATTTCCA                                                                                                                                <  2:360684/149‑1                               CGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGT                                                                                                                       <  2:182074/149‑1                                    GAAAGTAAAAATGCACATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCA                                                                                                                  <  2:187217/149‑1                                    GAAAGAAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCA                                                                                                                  <  2:187245/149‑1                                            AAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCGTATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCC                                                                                                          <  2:183830/149‑1                                                  ATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACA                                                                                                    >  1:405330/1‑149                                                   TATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAA                                                                                                   <  1:79390/149‑1                                                         TTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTGCCACTTAACCTATTAGAAGCCAGC                                                                                             >  1:266174/1‑149                                                              CTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCACATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCTATTACAAGCCCGCTACCG                                                                                        >  1:619795/1‑149                                                                              CATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTCCAACCCCGCTGCCGCAGATATTCCCGTGGC                                                                        >  1:217595/1‑149                                                                                 tggTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAG                                                                     <  1:779372/146‑1                                                                                   TTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATTCGTTATCACTTAAGCCATTACAAGCCAGCTGCCGCAGATATTCTCGTGTCGAGgg                                                                   >  2:19389/1‑147                                                                                   TTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCG                                                                   >  1:479675/1‑149                                                                                   TTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCG                                                                   >  2:761454/1‑149                                                                                   TTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTGACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAACCCGCTGCCGCAGATCTTCCCGTCGCGAGCG                                                                   >  2:19363/1‑149                                                                                        TTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGTATCGCATATCTATTATGTTAGTGGATTTGCTCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGCCATGCGATAAC                                                              >  2:297062/1‑149                                                                                         TATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACC                                                             >  1:102926/1‑149                                                                                           TAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCA                                                           >  2:580837/1‑149                                                                                              TGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCG                                                        <  2:107494/149‑1                                                                                                  TGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCCCT                                                    >  2:27508/1‑149                                                                                                        AGATCACAGAATAAATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTCCAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCCCTATGCGG                                              >  2:55062/1‑149                                                                                                          agCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATCTTTCCAGACATCTGTTATCACTTAACCCATTACTAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGAT                                            <  2:90194/147‑1                                                                                                          ATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGAT                                            >  1:530082/1‑149                                                                                                          ATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGAT                                            >  1:529991/1‑149                                                                                                           TCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATG                                           <  1:606885/149‑1                                                                                                            CACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGC                                          <  2:135197/149‑1                                                                                                             ACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCAAGCGCACTATGCGGATGCC                                         >  1:256821/1‑149                                                                                                              CAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCGCTATGCGGATGCCA                                        >  2:305422/1‑149                                                                                                               AGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTCTTGTCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGAGGCCAT                                       >  1:484189/1‑149                                                                                                                   cagATCTTCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGT                                   <  1:252256/146‑1                                                                                                                          TCAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATG                            <  1:335375/149‑1                                                                                                                           CAGGGATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGC                           >  2:38775/1‑149                                                                                                                                ATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATGTTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAA                      <  1:23973/149‑1                                                                                                                                ATCGCATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAA                      <  2:321761/149‑1                                                                                                                                   GCATATCTATTAAGTTTCTGTTTTTGCGGCTATATTTCGAGACATCTGTTATCACTTAATCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGa                   >  2:589677/1‑148                                                                                                                                     ATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT                 >  1:711653/1‑149                                                                                                                                     ATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT                 >  1:336551/1‑149                                                                                                                                     ATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT                 <  1:409108/149‑1                                                                                                                                     ATATCTATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCT                 <  1:469791/149‑1                                                                                                                                         cgATTAAGTTACTGGATTTGCCCCTATATTGCCAGACATCTGTTATCATTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGTGGATGCCATTCGTTATAATGCTCGAACGCCTCTGC             <  2:217595/147‑1                                                                                                                                           ATTAAGTTACTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAA           <  2:689697/149‑1                                                                                                                                                    CTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGGGCACTATGCGGATGCCATTCGTTATAATGCTCGCACGCACCTGCAAGGGTCTTTG  >  1:135135/1‑149                                                                                                                                                    CTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  >  2:609225/1‑149                                                                                                                                                                                                                                                                                                          TGTGCCTCCCTGGCAGTTTCATCCGGAACCCGGACGAAAGTAAAAATGCATATGAGTTGCACTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/2406715‑2406863 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTG  >  NC_000913/2996360‑2996506

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.