New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2406857 =	0 (0.000)	38 (0.850)	32/274	NT	100%	intergenic (‑218/‑702)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
	?	NC_000913	= 2997688	NA (NA)					intergenic (‑90/+2)	insC1/ygeQ	IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant

GGATCCCTGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2407001‑2406857 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  <  NC_000913/2997688‑2997541                                                                                                                                                                                                                                                                                                       GGATCCCTGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACACGGACTCACATTTACATTTATACAAACACACGAATGTAATAAATAGAAAAGAGTGAGTAACTAGAC                                                                                                                                                  >  1:32870/1‑149        TGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCC                                                                                                                                           >  2:297388/1‑149            CTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGA                                                                                                                                       >  1:784257/1‑149                  GCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCC                                                                                                                                 <  1:634431/149‑1                  GCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCC                                                                                                                                 <  2:61210/149‑1                   CCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCA                                                                                                                                <  1:316876/149‑1                     GCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGA                                                                                                                              >  2:344375/1‑149                     GCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGA                                                                                                                              <  1:489286/149‑1                        cCACCATTGCTGTTGGTACGGGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATCTCATACATAGAAGAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                           <  2:566186/148‑1                        TCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                           <  2:450971/149‑1                        TCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAA                                                                                                                           <  2:366216/149‑1                                  TGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACGAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAACATCAC                                                                                                                 >  2:81788/1‑149                                  TGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCCTAAATAGAAAAGAGTGAGTAACTAGACGGGCCCCCTGAATCTCCAGACAACCAATtgaac                                                                                                                 >  2:353664/1‑144                                    TTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTT                                                                                                               >  2:310996/1‑149                                      GGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAA                                                                                                             >  1:317082/1‑149                                       GTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTAAAA                                                                                                            >  1:61186/1‑149                                            TGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACAAGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCGAGACAACGAATATAACTTAAATAAGT                                                                                                       >  2:158008/1‑149                                              TTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGA                                                                                                     <  1:188975/149‑1                                              TTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGAACTCACATTTACATTTATACAAACACGCGCATGTCCTAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGA                                                                                                     <  1:164285/149‑1                                                 GCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAG                                                                                                  >  1:12195/1‑149                                                          CAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCGTGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATAC                                                                                         >  1:532277/1‑149                                                          CAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATAC                                                                                         >  2:300762/1‑149                                                                      ACGAGAGTGGAACAAGGACTCACAATTACATTTATACAAACACGCGCATGTCATAAATAGCAAAGAATGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTAAAATAAGTGATAGTCTTAATACTAATTTTTAGAC                                                                             >  2:750225/1‑149                                                                             TGGAACAAGGACTCACATTTACATTTATACAAACGCGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGATTTTGGACTAGTCAT                                                                      >  1:599218/1‑149                                                                              GGAACAAGGAACCACATCTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATT                                                                     <  1:700653/149‑1                                                                                AACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACAAATATCACTTAAATAAGTGATAGTCTTACTACTAGTTTTTAAACTAGGCATTGG                                                                   >  2:284729/1‑149                                                                                 ACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGGGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGATTTTAGACTAGTCATTGGA                                                                  >  1:689213/1‑149                                                                                           ACATTTACATTTATACAAACACGCGCATGTGATAAATAGCAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTATTTAGCACAGTCAGTGTAGAACAGATGg                                                        >  1:413818/1‑148                                                                                             ATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGCAGATT                                                      >  2:216577/1‑149                                                                                             ATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATT                                                      <  1:344375/149‑1                                                                                                TACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTATTTAGACTAGTCATTGGAGAACAGATGATTGAT                                                   <  1:510205/149‑1                                                                                                     TTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTGACTAGACTGGCCCCCTGAATCGCCAGACAACCAATAACACTTAAATAAGTGATAGTCTTAATCCTAGTTTTTAGACTAGTCAGTGAAGAACTAATGATGGATGgttt                                              >  1:719908/1‑145                                                                                                       ATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAG                                            <  2:649279/149‑1                                                                                                              CACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGACTCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGA                                     <  2:103233/149‑1                                                                                                                  CGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAA                                 <  2:784257/149‑1                                                                                                                    CATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGGTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTGTTGAGGCCGGAGAAGCG                               >  1:415383/1‑149                                                                                                                          ATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGCGAAACGCAGCCG                         >  2:753403/1‑149                                                                                                                            AAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGC                       >  1:276423/1‑149                                                                                                                                  AAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCA                 <  1:714595/149‑1                                                                                                                                            GTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA       <  1:310996/149‑1                                                                                                                                             TAACTAGACTGGCCCCCTGAATCCCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAAAACTTGATCTATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAG      <  1:158008/149‑1                                                                                                                                               ACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTCGGGCCGGAGAAACGCAGACGGCGTACCAACCAGGAAAAGAT    >  2:365694/1‑149                                                                                                                                               ACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCGCACAGGAAAAGAT    >  2:767280/1‑149                                                                                                                                               ACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGAT    <  2:762586/149‑1                                                                                                                                                CTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC   <  1:799046/149‑1                                                                                                                                                 TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCCCTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  <  1:282981/149‑1                                                                                                                                                 TAGACTGGCCCCCTGAAGCTCCAGACACCCAATTGCCCTTAAAGAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  <  1:149457/149‑1                                                                                                                                                                                                                                                                                                       GGATCCCTGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2407001‑2406857 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  <  NC_000913/2997688‑2997541

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.