New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2270512 =	168 (0.880)	14 (0.080)	9/144	NT	9.0%	intergenic (‑155/+77)	ylmA/glmS	putative ABC transporter ATP‑binding protein YlmA/Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]
	?	USA300TCH1516_ALE	2270545 =	133 (0.780)					intergenic (‑188/+44)	ylmA/glmS	putative ABC transporter ATP‑binding protein YlmA/Glutamine‑‑fructose‑6‑phosphate aminotransferase [isomerizing]

AAATCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2270609‑2270512 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagggtgcCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAACA  >  USA300TCH1516_ALE/2270545‑2270634                                                                                                                                                                                              AAATCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGA                                                                                                   >  2:1303102/1‑91  AATGAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAA                                                                                                  <  1:3056832/91‑1  AATCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAA                                                                                                  >  2:3416000/1‑91  AATCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAA                                                                                                  >  2:3416324/1‑91   ATCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAG                                                                                                 <  2:1676923/91‑1    TCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGG                                                                                                <  1:962470/91‑1    TCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGG                                                                                                <  1:1775973/91‑1     CAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGG                                                                                               <  1:62545/91‑1     CAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGG                                                                                               <  2:736381/91‑1     CAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGG                                                                                               <  2:1039945/91‑1      AGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGT                                                                                              <  1:2443979/91‑1       GTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTG                                                                                             <  1:3789295/91‑1       GTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTG                                                                                             >  1:304675/1‑91        TTACTGTGGAATAATTCACTTTTTTAGAATCGATCATGTATTAAGATTAAAGTGTATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC                                                                                            <  1:1169537/91‑1        TTACTGTGGAATAATTCACTTTTTTAGAATCGATCATGTATTAAGATTAAAGTGTATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC                                                                                            <  1:1169452/91‑1        TTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC                                                                                            <  1:482924/91‑1        TTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC                                                                                            >  1:3868867/1‑91        TTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC                                                                                            <  2:3808156/91‑1        TTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC                                                                                            <  1:1104393/91‑1            TGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTG                                                                                             >  2:3642992/1‑86            TGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTG                                                                                             <  1:3642992/86‑1                                                TTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAG                                                    >  1:1005048/1‑91                                                         AAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATT                                           >  1:3297888/1‑91                                                         AAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTCTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATT                                           >  1:3297898/1‑91                                                         AAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGG                                                                                                <  1:3509078/38‑1                                                         AAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGG                                                                                                >  2:3509078/1‑38                                                            TATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCA                                        >  1:2191356/1‑91                                                            TATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCA                                        >  1:2191267/1‑91                                                            TATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCA                                        >  1:2191234/1‑91                                                             ATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCAC                                       >  1:2990043/1‑91                                                             ATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCAC                                       >  1:2989023/1‑91                                                              TATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACA                                      >  1:1324102/1‑91                                                                    ACCCTTTTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACT                                >  2:1878018/1‑91                                                                          TTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTA                          >  1:3763717/1‑91                                                                          TTAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTA                          >  1:1746312/1‑91                                                                           TAGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAG                         >  2:3158267/1‑91                                                                            AGATTAATCGACTAGAAGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGC                        >  1:1086354/1‑91                                                                                         aaacGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGT           <  1:3127511/87‑1                                                                                            AGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTA        <  1:2752945/91‑1                                                                                            AGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTA        >  2:3423647/1‑91                                                                                            AGGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTA        <  1:2753042/91‑1                                                                                             GGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTAT       >  1:938628/1‑91                                                                                             GGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTAT       >  1:938730/1‑91                                                                                             GGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTAT       >  1:3534179/1‑91                                                                                             GGGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTAT       >  1:3375148/1‑91                                                                                              GGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATC      <  2:1641561/91‑1                                                                                              GGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATC      >  1:3440070/1‑91                                                                                              GGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATC      >  2:3748008/1‑91                                                                                              GGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATC      <  1:2625785/91‑1                                                                                              GGTGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGAGAACTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTCTC      >  2:1385237/1‑91                                                                                                TGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAA    >  2:767848/1‑91                                                                                                TGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAA    >  2:767623/1‑91                                                                                                TGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAA    <  2:384907/91‑1                                                                                                TGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAA    <  2:2504813/91‑1                                                                                                TGCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAA    >  2:122567/1‑91                                                                                                 GCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAAC   <  2:190301/91‑1                                                                                                 GCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAAC   <  2:187082/91‑1                                                                                                 GCCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAAC   >  1:599478/1‑91                                                                                                 GCCATATACTTTAATTTTAATACATGAGTGATTCTAAAAAAGTGAATTATTCCACAGTAGCTGATTTAGCAAGGTTACGTGGTTTATCAAC   <  2:2214522/91‑1                                                                                                  CCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAACA  <  2:2370965/91‑1                                                                                                  CCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAACA  <  1:2446679/91‑1                                                                                                  CCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAACA  <  1:1462204/91‑1                                                                                                                                                                                              AAATCAGTTACTGTGGAATAATTCACTTTTTTAGAATCAATCATGTATTAAAATTAAAGTATATGGCACCCTTTTAGATTAATCGACTAGAAGGGTGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2270609‑2270512 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagggtgcCATATACTTTAATTTTAATACATGATTGATTCTAAAAAAGTGAATTATTCCACAGTAACTGATTTAGCAAGGTTACGTGGTTTATCAACA  >  USA300TCH1516_ALE/2270545‑2270634

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.