New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	257908 =	NA (NA)	52 (0.770)	48/284	0.3	96.3%	intergenic (+9/‑768)	crl/crl	pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers
	?	NC_000913	= 1293039	2 (0.030)					intergenic (‑117/‑488)	hns/tdk	global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase

CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/258048‑257908 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTG  <  NC_000913/1293039‑1292899                                                                                                                                                                                                                                                                                            CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACACAGTCATCGGGCATTATCTGAACATAAAACACTATCAATACGTTGGAGTCATTACCCG                                                                                                                                             >  1:390965/1‑143    CATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGGGCA                                                                                                                                          >  1:23390/1‑143        ACCTGAATCCGCGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAA                                                                                                                                      <  1:1023358/143‑1           TGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATA                                                                                                                                   >  1:734652/1‑143             aacCTGAGGCAGCACCTGGCACGGCGGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAA                                                                                                                                 <  2:1148941/140‑1              ATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTTTCAAAATCGGTGGAGCTGCATGACAAAGTCATCTGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAG                                                                                                                                <  2:67736/143‑1               TCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGA                                                                                                                               <  1:1174869/143‑1                          ACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAA                                                                                                                    <  2:100355/143‑1                            CTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATACGTTGGAGTCATTACCCGGCTCAAACTCAAGAACACTTTTGCATT                                                                                                                  >  2:837536/1‑143                              GGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGATCATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCC                                                                                                                <  2:571125/143‑1                                 ACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCAGGCAAAAAATAAAGAACAAAATTGAATACATTA                                                                                                             >  1:235644/1‑143                                   GGCTGGGACGTGAGTCGCTGTCGTGTTCAAAATCGGTGGAGCTGCAGGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACA                                                                                                           <  2:963794/143‑1                                   GGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACA                                                                                                           >  1:758472/1‑143                                         GACGGAAGTCGCTGTCGTGCTCCAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTG                                                                                                     <  1:928155/143‑1                                               gGTCGCTGGCGTGTTCCCAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACATTATCGATATGTTGTAGTCATTCCCCGGCACAAAATAAAGAACAATTTTGCATTCCTTACCTTTCTGGCTATT                                                                                               <  2:658733/142‑1                                                  CGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACGTAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATCCCTGGCTATCGCA                                                                                            >  2:371153/1‑143                                                    CTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCCGGACATAAAACATTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACA                                                                                          >  1:220277/1‑143                                                     TGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAA                                                                                         <  1:543493/143‑1                                                       TCGTTCTCAAAATCGGGGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACCCTATCAATAAGGTGGAGTCATTACCCGGCACACAATAAAGAACAATTTAAAATTCCTGACCGTCCTGGCTAGTGaccgaca                                                                                       >  2:62202/1‑136                                                         GTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGGTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGA                                                                                     >  2:851756/1‑143                                                               AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAA                                                                               <  1:1125169/143‑1                                                                 AATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGG                                                                             <  1:1143860/143‑1                                                                      GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTGCACGGCACATAATAAAGAACAATTTTGAATTCCTTACATTCCTGTCTAGTGCACAACTGAATTTAAGACTCTA                                                                        >  2:77957/1‑143                                                                       TGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTAT                                                                       <  1:984923/143‑1                                                                           GCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATT                                                                   >  1:878653/1‑143                                                                              GCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGGTGGAGTCATTAGCAGGCACAAAATAAAGAACGATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATCTACGGCTCTATTATTAac                                                                >  2:1158527/1‑141                                                                                ATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTC                                                              <  1:975417/143‑1                                                                                  GACAGAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAA                                                            <  1:294779/143‑1                                                                                  GACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCCATAAGTTGGAGTCATTACACGGCACAAAATAAAGAACAATTCTGAATTCCTTACATTCCTGGCCATTGCACAACTGAATCTAACGATCTATTATTACCCCAA                                                            >  2:1088086/1‑143                                                                                     AAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAA                                                         >  1:936397/1‑143                                                                                       AGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCGCTATTATTCCCTCCACCAAC                                                       >  1:1141036/1‑143                                                                                             CGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCC                                                 >  2:455662/1‑143                                                                                                  ATTATCTGAACATAAAACACTATCAATAAGATGGAGTCATGACCCGGCACAAAATAAAGAACAATGTTGAATTCCTTACATTCCTGGCTATTGCACAGCTGAATTTAAGGCTCTATTATTATCTCAACAAACCACCCCAAGAT                                            >  1:868884/1‑143                                                                                                    TATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAA                                          <  1:437682/143‑1                                                                                                    TATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAA                                          <  1:122494/143‑1                                                                                                       CTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAACATCAAGCAAAATGTTGAATTGATCAAAAACGTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTT                                       >  1:861827/1‑143                                                                                                        TGAACATAAAACACTATCAATAAGTTGGAGTCATTACACGGCACAAAATAAAGAACAATATTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTAGCTCAACACACCAGCCCAAGATAAGTTT                                      >  1:382612/1‑143                                                                                                        TGAACATAAAACACCATCCATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTT                                      <  1:361779/143‑1                                                                                                               AAAACACTATCAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTA                               >  1:529044/1‑143                                                                                                                  tCACTGTCGATAAGTGGGAGTCATTACACGTGACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTA                            <  2:41386/142‑1                                                                                                                         CAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACACTTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATATAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAG                     >  1:781959/1‑143                                                                                                                         CAATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCACTATAAGTTTGAGATTACTACAACGAG                     >  1:228465/1‑143                                                                                                                          AATAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACATCAACCAACCACCCCAATATAAGTTTGAGATTACTACCATGAGC                    >  2:1050097/1‑143                                                                                                                            TAAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGGATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGA                  >  1:647051/1‑143                                                                                                                             AAGTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAA                 <  2:878653/143‑1                                                                                                                               GTTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCCATATAAGTTTGAGATTACTACAATGAGCGAAGC               >  1:140885/1‑143                                                                                                                                TTGGAGTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCCACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCA              <  2:172660/143‑1                                                                                                                                     GTCATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACCTTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCCACAAACCACCCCAATATAAGTTTGAGATTACGACAATGACCGACACACTAAA         >  2:466240/1‑143                                                                                                                                        ATTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAAT      <  1:585133/143‑1                                                                                                                                         TTACCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATCTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATT     <  1:439203/143‑1                                                                                                                                           ACCCGGCACAAACTAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCT   <  1:30038/143‑1                                                                                                                                            CCCGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTG  <  1:352782/143‑1                                                                                                                                                                                                                                                                                            CGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/258048‑257908 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGGCACAAAATAAAGAACAATTTTGAATTCCTTACATTCCTGGCTATTGCACAACTGAATTTAAGGCTCTATTATTACCTCAACAAACCACCCCAATATAAGTTTGAGATTACTACAATGAGCGAAGCACTTAAAATTCTG  <  NC_000913/1293039‑1292899

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.