Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	618,513	IS5 (+) +4 bp	coding (260‑263/1134 nt)	fepE →	regulator of length of O‑antigen component of lipopolysaccharide chains

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	273955 =	NA (NA)	44 (1.180)	38/284	0.1	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	618513 =	0 (0.000)					coding (260/1134 nt)	fepE	regulator of length of O‑antigen component of lipopolysaccharide chains
*	?	NC_000913	= 275149	NA (NA)	40 (1.080)	31/282	0.2	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 618516	0 (0.000)					coding (263/1134 nt)	fepE	regulator of length of O‑antigen component of lipopolysaccharide chains

GGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/274094‑273955 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGC  >  NC_000913/618513‑618654                                                                                                                                                                                                                                                                                            ggcATAACCACTTAAATGGCGAAGACACGGTCTAAACAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTA                                                                                                                                             <  1:662925/140‑1           CTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTGGCACCTTCCCTACGCATCGTGT                                                                                                                                   >  2:217424/1‑143           CTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGT                                                                                                                                   <  2:282695/143‑1            TTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGGCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTG                                                                                                                                  >  1:319106/1‑143                      AAGGAACGGGCGAAATGGGCGGGTGCGAGGCATGTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGCAGCATTTCACCGTTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGG                                                                                                                        <  1:461683/143‑1                      AAGAAACGGTCTAAATAGGCTGCTTCAAGGCATTTACGGGAGAAACAATCGGCTCAAACATGAAGAAATGAAATGACTGCGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGG                                                                                                                        <  1:271561/143‑1                      AAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTAATTCGCACCGTCCACAAGCTTCGTGTGCGGGATCTGG                                                                                                                        >  2:475620/1‑143                      AAGAAACGGTCGAAATAGGCTGGTTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGGGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGG                                                                                                                        <  2:119356/143‑1                                   AATAGGCTGATTCAAGGCATTTACGGGAGAAAAAAACGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAActcga                                                                                                           >  2:540683/1‑138                                    ATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGAT                                                                                                          <  1:333928/143‑1                                        GCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTACCTAAGCGTAGTGTGCTGGGTCTGGCTACCCAAAGCGATCGca                                                                                                      >  2:637263/1‑141                                         CTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGCGTCGGCCGAGAAGGATTTCCCCGCTTATTCGCACCTTCCCTACGCTTCGTGTGCTGGATCTGGATATCAGAATTGATCGTcc                                                                                                     >  1:77630/1‑141                                           GATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCGGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAG                                                                                                   >  1:438761/1‑143                                             TTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAA                                                                                                 <  1:436844/143‑1                                                 AGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGACATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTACGCTTCGTGTGCTGGATCTGGATATCAAAACTGATCGCACAGAAGCAa                                                                                             >  2:127789/1‑142                                                     ATTTACGGGAGAAAAAAACGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAA                                                                                         <  1:411835/143‑1                                                      TTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAAC                                                                                        >  1:581112/1‑143                                                       TTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACC                                                                                       <  1:309814/143‑1                                                          CGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGAACAGCCTTAAGAGCAAAATTGATCGTACAGAAGCATTTAACCTGT                                                                                    >  2:652386/1‑143                                                           GGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCATAAGCTTCGTGTGATGGATCTGGATATCAAACTTGAACGTGTAGAAGCAGTTAACATGTT                                                                                   >  2:538968/1‑143                                                                 AAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAA                                                                             <  2:607890/143‑1                                                                 AAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAA                                                                             <  1:24594/143‑1                                                                    AATGGGCTGAAAGCTGAAGAGATGGACTGACTGAGTCAGCCGAGAAGAATTTCCCCGGTTATTCGCACCTACCCTAAGCTTCGGGGGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATGTAACCTGTGTATCAAGAA                                                                          <  2:25810/143‑1                                                                     ATCGGCTCAATCATGAAGAAATGAAATTACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAG                                                                         <  2:207409/143‑1                                                                     ATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTACTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAG                                                                         <  1:28899/143‑1                                                                        GGCTCAAACATGAAGAACTGAAAGGACTGAGTCAGCCGAGAAGACTTTCCCCGCTGATTCGCACCTTCGCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTT                                                                      <  2:192420/143‑1                                                                          CTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCA                                                                    <  2:281615/143‑1                                                                             AAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCACAATTGATCGTACAGAAGCATTTAACCGGGTTCTCCAGAAGTTGCAGTg                                                                 >  2:438208/1‑142                                                                                CATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGT                                                              <  1:229462/143‑1                                                                                 ATGAAGAGATGAAATGACTGAGTCAGCCGAGAAGACTTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTT                                                             <  1:213919/143‑1                                                                                              ATGACTGGGTGAGCAGAGGAGGATTTCCCCGCTTGTTCGCACCTTCCGTAAGCGTCGTGTGCTGGATCTGGATATCAAAATTGATCGGACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAG                                                <  2:430774/143‑1                                                                                              ATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAG                                                >  1:327756/1‑143                                                                                                       TCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGC                                       >  1:9293/1‑143                                                                                                         AGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGT                                     <  2:152752/143‑1                                                                                                              AGAAGTATTTCCCCGCGTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATC                                <  1:88521/143‑1                                                                                                              AGAAGAATTGCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATC                                <  2:94264/143‑1                                                                                                               gaacagTTTCCCCGCCTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACACAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCA                               <  2:136592/137‑1                                                                                                                  GAATTTCCCCGCTTATTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTCCATTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCT                            >  1:213451/1‑143                                                                                                                     ttgCCCCGCTTAGTCGCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTAT                         <  2:122125/140‑1                                                                                                                           ggaTTATTCGCACCTTCTCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACATGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATG                   <  2:306573/140‑1                                                                                                                                 TTCGCACCTTCCCTAAGCTTCGTGTGCTGGATTTGTTTACCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAA             >  2:370823/1‑143                                                                                                                                    GCACCTTCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTCTGTTATGGCCCACTTA          >  1:365117/1‑143                                                                                                                                         tgCCCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGA     <  2:500683/141‑1                                                                                                                                            CCTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGC  >  2:450047/1‑143                                                                                                                                                                                                                                                                                            GGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/274094‑273955 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAGCTTCGTGTGCTGGATCTGGATATCAAAATTGATCGTACAGAAGCATTTAACCTGTTTATCAAGAAGTTTCAGTCGGTTAGCTTGCTGGAAGAGTACCTGCGTTCATCACCTTATGTGATGGACCAATTAAAAGAGGC  >  NC_000913/618513‑618654

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.