New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2406857 =	0 (0.000)	39 (0.900)	30/274	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

CGGATCCCTGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2407002‑2406857 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  <  NC_000913/2997688‑2997541                                                                                                                                                                                                                                                                                                        CGGATCCCTGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGA                                                                                                                                                   >  1:310186/1‑149            tcgTGATGCCGCCTCACCATTGCTGTTGGTACGTTTTCTCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTG                                                                                                                                        <  1:339179/146‑1              TTGATGCCGCCTCACCATTGCTGTTGATACGTGCTAGCGGATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCACGTCATAAATAGAAAAGAGTGAGCAACTAGACTGGCCGCCTGAA                                                                                                                                      >  2:134402/1‑149                  TGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAGGAGTGAGTAACTAAACTGGCCCCCTGAATGTC                                                                                                                                  >  1:112693/1‑149                                     TTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAGAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCAATT                                                                                                               >  1:441129/1‑149                                        GTACGAGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAA                                                                                                            >  1:778605/1‑149                                         TACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAAT                                                                                                           <  2:310186/149‑1                                                     TATGACCAGCGATGCTGCACGAGAGTGGAACAAGGCCTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCT                                                                                               <  2:429761/149‑1                                                      ATGACCAGCGATGCTGCACGAGAGTGGAACATGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGCGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTT                                                                                              <  1:525627/149‑1                                                      ATGACCAGAGATGCTGCACGAGAATGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACGAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTT                                                                                              <  1:153146/149‑1                                                        GACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTACATAAGTGATAGTCGTAA                                                                                            >  2:529519/1‑149                                                         ACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAGGGGATAGTCTTAAT                                                                                           >  2:31718/1‑149                                                         ACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAAT                                                                                           >  2:699194/1‑149                                                             GCGATGCTTCACGAGAGGGGAACAAGGACGCACAATTACATTTCTACGAACACTCGAATGTAATAAATAGAAAAGAGTGAGTAACTAGACTGCCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTA                                                                                       <  1:105274/149‑1                                                             GCGATGCTGAACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTA                                                                                       <  1:231570/149‑1                                                                   CTGTACGAGAGTGGAACAAATACCCACCTTTACCTTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTT                                                                                 <  1:37734/149‑1                                                                    TGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAACTAAGTGATAGTCTTAATACTAGTTTTTA                                                                                <  1:469713/149‑1                                                                    TGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTA                                                                                <  1:40732/149‑1                                                                      CACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGA                                                                              >  2:447199/1‑149                                                                       ACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGAGCCCTGGTCCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGAC                                                                             >  1:768594/1‑149                                                                         GAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTA                                                                           <  1:639612/149‑1                                                                             GTGGAAGAAGGACTGAGATGTACATGTATACAAACACGCGGATGGCATAAATAGAAAAGAGGGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCA                                                                       <  1:233371/149‑1                                                                                 AACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAGGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACACCCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTGTTAGACTAGTCATTGG                                                                   >  1:35285/1‑149                                                                                 AACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGG                                                                   <  2:778605/149‑1                                                                                   CAAGGACTCCCATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAG                                                                 <  1:273978/149‑1                                                                                              ATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTATTAATAATAGTTTTTAGACTTGTCATTGGAGAACAGATGATT                                                      >  1:555967/1‑149                                                                                                    acTTATACAAGCACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATCTCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTC                                                <  1:597232/147‑1                                                                                                      TTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTT                                              >  2:386735/1‑149                                                                                                                      ATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGC                              >  1:712810/1‑149                                                                                                                      ATGTCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATACCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGC                              >  1:607982/1‑149                                                                                                                         TCATAAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTTGACTAGTCATTGGAGAACAGATGCTTGATGTCTTAGGGCCGGAGAAACGCAGA                           <  1:478783/149‑1                                                                                                                           ATAAATAGAAAAGAGTGAGTAACTAGACTTGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAACCGCAGACG                         <  2:112693/149‑1                                                                                                                             AAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCCCTTAAATCAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGACACGCAGACGGC                       >  1:54123/1‑149                                                                                                                             AAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGCTGGTGGATGTCTTAGGGCAGGAGAAACGCAGAgaga                       >  1:248247/1‑145                                                                                                                             AAATAGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGC                       >  1:225124/1‑149                                                                                                                                 AGAAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCACTATCACTTAAATAAGCGATAGTCTTAATACTAGTCTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTAC                   <  2:280757/149‑1                                                                                                                                   AAAAGAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCA                 >  2:365377/1‑149                                                                                                                                   AAAAGAGTGAGTAACAAGTCTGGCCCCCTGAATCTCCAGATAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGACCGGAGAAACGCAGACGGCGTACCc                 >  1:575594/1‑148                                                                                                                                       GAGTGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGTAGAACAGATGATTGATGTCTTAGGGCCGGAGGAACGCAGACGGCGTACCACACA             >  2:374718/1‑149                                                                                                                                       GAGAGAGTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCGTAGGGCCGGAGAAACGCAGACGGCGTACCACACA             >  2:483227/1‑149                                                                                                                                             GTAACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAA       >  1:528391/1‑149                                                                                                                                                ACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAACGAT    >  1:264539/1‑149                                                                                                                                                 CTAGACTGGCTCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATC   <  1:342631/149‑1                                                                                                                                                  TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATCGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  >  2:68696/1‑149                                                                                                                                                  TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGGTCG  >  1:362413/1‑149                                                                                                                                                  TAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCG  >  1:344974/1‑149                                                                                                                                                                                                                                                                                                        CGGATCCCTGCTCTTGATGCCGCCTCACCATTGCTGTTGGTACGTGTTCGCGTATGACCAGCGATGCTGCACGAGAGTGGAACAAGGACTCACATTTACATTTATACAAACACGCGCATGTCATAAATAGAAAAGAGTGAGTAACT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/2407002‑2406857 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑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.