New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2684290	146 (0.720)	17 (0.100)	9/136	NT	11.5%	intergenic (+49/+121)	mvaS/ogt	Hydroxymethylglutaryl‑CoA synthase/Methylated‑DNA‑‑protein‑cysteine methyltransferase
	?	USA300TCH1516_ALE	= 2684307	138 (0.800)					intergenic (+66/+104)	mvaS/ogt	Hydroxymethylglutaryl‑CoA synthase/Methylated‑DNA‑‑protein‑cysteine methyltransferase

CTACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2684190‑2684290 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagcagtaagacGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGATATTCAC  <  USA300TCH1516_ALE/2684307‑2684219                                                                                                                                                                                                CTACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCA                                                                                                     >  1:2777353/1‑91  TACTTATCAAATATTGAAAATAACGTTCGTGAATATCTCAGACCAGCGTAGTCTGTGTATTTAAAACACATATAATAAAACCTAAAAGCAG                                                                                                    >  2:2775887/1‑91  TACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAG                                                                                                    >  2:1017706/1‑91  TACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAG                                                                                                    >  2:2775969/1‑91   ACTTCTCAAATATTGAAAATAACGTGCGTGAATATCACAGACCAGAGTAGTCGGTGTACTTAAAACACATATAATAACACCTAAAAGCAGC                                                                                                   >  2:1484858/1‑91   ACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGC                                                                                                   >  2:2779358/1‑91   ACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGC                                                                                                   >  1:2008712/1‑91   ACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGC                                                                                                   >  2:2877735/1‑91     TTATCAAATATAGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAG                                                                                                 <  2:388465/91‑1      TATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGT                                                                                                >  1:3001223/1‑91      TATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGT                                                                                                <  2:494742/91‑1       ATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTA                                                                                               >  1:3648515/1‑91       ATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTA                                                                                               >  1:387804/1‑91        TCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAA                                                                                              >  2:3942947/1‑91         CAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAG                                                                                             <  2:3499784/91‑1         CAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAG                                                                                             >  2:870658/1‑91           AATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGAC                                                                                           <  2:1281981/91‑1           AATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGAC                                                                                           <  2:976969/91‑1                      TAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTA                                                                                <  2:2074163/91‑1                      TAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTA                                                                                <  2:2073487/91‑1                           TTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGT                                                                           <  1:2725094/91‑1                            TCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTG                                                                          <  1:2896962/91‑1                             CGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGG                                                                         <  1:1774974/91‑1                             CGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGG                                                                         <  2:3829745/91‑1                             CGTAAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGATGTGG                                                                         <  1:3121452/91‑1                              GTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGT                                                                        <  1:3809828/91‑1                              GTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGT                                                                        <  1:3626001/91‑1                              GTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGT                                                                        <  2:2227701/91‑1                                GAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCT                                                                      <  1:1904488/91‑1                                GAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCT                                                                      <  1:247557/91‑1                                  ATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTA                                                                    <  2:3210912/91‑1                                     TCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTG                                                                 <  1:1901104/91‑1                                     TCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTG                                                                 <  1:1901118/91‑1                                     TCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTG                                                                 <  1:1901144/91‑1                                                                      CATATAATAAAACCTAAAAGCAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAAT                                >  2:3402675/1‑91                                                                                          CAGCAGTAAGGCGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTG            <  1:1784062/91‑1                                                                                          CAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTG            <  1:1711936/91‑1                                                                                          CAGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTG            <  2:2130216/91‑1                                                                                           AGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGT           <  1:346439/91‑1                                                                                           AGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGT           >  1:3574673/1‑91                                                                                           AGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGT           >  1:3574933/1‑91                                                                                           AGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGT           <  2:1261399/91‑1                                                                                           AGCAGTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGATTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGg           >  2:53831/1‑90                                                                                              AGTAAGACGGTTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGAT        <  1:3788171/91‑1                                                                                               GTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGATA       >  2:1005018/1‑91                                                                                               GTAAGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGATA       <  1:519515/91‑1                                                                                                  AGACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGATATTC    >  1:3854860/1‑91                                                                                                    ACGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGATATTCAC  >  2:2349975/1‑91                                                                                                                                                                                                CTACTTATCAAATATTGAAAATAACGTTCGTGAATATCACAGACCAGAGTAGTCGGTGTATTTAAAACACATATAATAAAACCTAAAAGCAGCAGTAAGAC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2684190‑2684290 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑cagcagtaagacGATTTCAATTAGAAGTGGTCTTACTGCTGCTTTTAGGTTTTATTATATGTGTTTTAAATACACCGACTACTCTGGTCTGTGATATTCAC  <  USA300TCH1516_ALE/2684307‑2684219

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