New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 282679	139 (0.730)	13 (0.080)	9/140	NT	8.7%	intergenic (‑430/‑143)	hmp/ldh1	Flavohemoprotein/L‑lactate dehydrogenase 1
	?	USA300TCH1516_ALE	= 282694	150 (0.900)					intergenic (‑445/‑128)	hmp/ldh1	Flavohemoprotein/L‑lactate dehydrogenase 1

AAAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/282580‑282679 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacttaaaagGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGATT  <  USA300TCH1516_ALE/282694‑282605                                                                                                                                                                                                AAAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAA                                                                                                     <  1:1686751/91‑1  AAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAA                                                                                                    <  2:898297/91‑1  AAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAA                                                                                                    >  1:2009912/1‑91  AAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAA                                                                                                    <  2:494819/91‑1  AAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAA                                                                                                    <  1:3241485/91‑1   AAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAAC                                                                                                   <  1:2021562/91‑1   AAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAAC                                                                                                   >  2:1969973/1‑91   AAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAAC                                                                                                   <  2:2767370/91‑1   AAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAAC                                                                                                   <  1:1302847/91‑1     ATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTT                                                                                                 <  1:3427098/91‑1      TTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTA                                                                                                >  1:1529422/1‑91      TTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTA                                                                                                <  2:3780526/91‑1        AAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAA                                                                                              >  2:2407358/1‑91        AAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAA                                                                                              <  1:948089/91‑1        AAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAA                                                                                              >  2:474422/1‑91        AAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAA                                                                                              <  1:2774537/91‑1         AAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAA                                                                                             >  2:448730/1‑91         AAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAA                                                                                             >  1:3762254/1‑91         AAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAA                                                                                             <  1:1146794/91‑1          AATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAG                                                                                            >  2:2863164/1‑91          AATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAG                                                                                            >  1:1793016/1‑91          AATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAG                                                                                            >  1:1793694/1‑91                     AAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCA                                                                                 <  1:132701/91‑1                     AAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCA                                                                                 <  1:133012/91‑1                         AAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCG                                                                             <  1:2650060/91‑1                             CACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTT                                                                         <  1:1458025/91‑1                              ACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTT                                                                        <  2:33933/91‑1                               CAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTA                                                                       <  1:3785291/91‑1                               CAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTA                                                                       <  1:3785579/91‑1                                AATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTAA                                                                      <  1:1973886/91‑1                                AATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTAA                                                                      <  2:2098961/91‑1                                     AATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTAAG                                                                     >  2:924649/1‑87                                     AATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTAAG                                                                     <  1:924649/87‑1                                         TTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGAT                                                             <  2:3230488/91‑1                                         TTGACCCAGTACGTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGAT                                                             <  2:3229589/91‑1                                                                                          tagCTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTA            <  2:1537157/88‑1                                                                                           AACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAA           >  1:2241230/1‑91                                                                                           AACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAA           <  2:509725/91‑1                                                                                           AACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAA           >  1:1720197/1‑91                                                                                           AACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAA           >  1:2283578/1‑91                                                                                            ACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAA          >  2:3114108/1‑91                                                                                            ACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAA          <  1:2366322/91‑1                                                                                            ACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAA          >  1:2586276/1‑91                                                                                            ACTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAA          <  2:1779571/91‑1                                                                                             CTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAAT         >  1:1940996/1‑91                                                                                             CTTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAAT         >  1:1801510/1‑91                                                                                              TTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATT        >  2:2906250/1‑91                                                                                              TTAAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATT        >  2:2645106/1‑91                                                                                                AAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATGTTAAATTGT      <  1:1446060/91‑1                                                                                                AAAAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGT      <  1:2266894/91‑1                                                                                                  AAGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGA    <  1:1382226/91‑1                                                                                                   AGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGAT   <  1:2451303/91‑1                                                                                                   AGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGAT   <  1:1530651/91‑1                                                                                                   AGGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGAT   >  1:1135988/1‑91                                                                                                    GGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGATT  >  2:816075/1‑91                                                                                                                                                                                                AAAAATTAAAATAAAATGTGAAATAAATCACAATTTAATATTGACCCAGTACTTAATGCATGTTACATTTTATATGTGAAATAAATCACAAACTTAAAAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/282580‑282679 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacttaaaagGTCATGTGTCATCCGCTTTTAAGTTTGTGATTTATTTCACATATAAAATGTAACATGCATTAAGTACTGGGTCAATATTAAATTGTGATT  <  USA300TCH1516_ALE/282694‑282605

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.