New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2464733	32 (1.070)	3 (0.110)	3/258	3.6	9.2%	intergenic (+29/+19)	gltS/fni	Sodium/glutamate symporter/Isopentenyl‑diphosphate delta‑isomerase
	?	USA300TCH1516_ALE	= 2464737	31 (1.180)					intergenic (+33/+15)	gltS/fni	Sodium/glutamate symporter/Isopentenyl‑diphosphate delta‑isomerase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ATATGGAAACTCACCTAAAGCATATTTAGTTGTACCTATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGATTTCATGTGT  >  USA300TCH1516_ALE/2464596‑2464881                                                                                                                                              |                                                                                                                                                 acatGGCAACTCCCCTAAAGCATATTTAGTTGTACCTATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGcctcc                                                                                                                                            <  1:77398/146‑1 (MQ=255)  tatGGAAACTCACCTAAAGCATATTTAGTTGTGCCTATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGcctcct                                                                                                                                           >  1:407510/1‑148 (MQ=255)       aaaCTCACCTAAAGCATATTTAGTTGTACCTATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCGAAGGCCTCCTCtttt                                                                                                                                      <  1:355785/148‑1 (MQ=255)                  aaGCATATTTAGTTGTACCTTTTGTTAGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCg                                                                                                                           <  1:12943/148‑1 (MQ=255)                  aaGCAGATTTAGTTGTACCTATTGTTGGGGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACCCCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCg                                                                                                                           <  1:435862/148‑1 (MQ=255)                     cATATTTAGTTGTACCGTTTGTTGGTGCATTCTTACTCGATTACATAGGAACGGCGACGGTTATGGGTTTCTTACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATg                                                                                                                        <  1:275041/148‑1 (MQ=255)                       tatTTAGTTGTACCTATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGta                                                                                                                      <  1:186588/148‑1 (MQ=255)                                   cccaTTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTAc                                                                                                          <  1:234966/145‑1 (MQ=255)                                     tATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACgt                                                                                                        <  1:75762/148‑1 (MQ=255)                                        tgttgGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCCCGATGTATATTCAAGTTACgttgt                                                                                                     <  1:316313/148‑1 (MQ=255)                                        tgttgGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATAAATACATTCGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACgttgt                                                                                                     <  1:432064/148‑1 (MQ=255)                                        tgttgGTGCATTCTTAATCGATTGAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACgttgt                                                                                                     <  1:346122/148‑1 (MQ=255)                                          ttgGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTc                                                                                                   >  1:597132/1‑148 (MQ=255)                                           tgGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCt                                                                                                  >  1:92723/1‑148 (MQ=255)                                           tgGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCt                                                                                                  <  1:126550/148‑1 (MQ=255)                                              tGCATTCTTAATCGATTTGATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATc                                                                                               >  1:464515/1‑148 (MQ=255)                                                 aTTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGCCGACAAGTCCACCGCCTCTTTTATTTATCCTCGATGAATATTCAAGTTACGTTATTCTATCCAt                                                                                            >  1:301097/1‑148 (MQ=255)                                                                 aTTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGAc                                                                            <  1:361769/148‑1 (MQ=255)                                                                 aTTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATACTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGAc                                                                            >  1:527347/1‑148 (MQ=255)                                                                       gtTATAGTCATTTTGGTATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATa                                                                      <  1:137593/148‑1 (MQ=255)                                                                         tataGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACg                                                                    <  1:395288/148‑1 (MQ=255)                                                                            aGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGAtt                                                                 >  1:81322/1‑148 (MQ=255)                                                                              tCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTAACCATGACACTTCTCCCGGACTAAATACGATTTg                                                               >  1:113776/1‑148 (MQ=255)                                                                                     gggATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTtgt                                                        >  1:5554/1‑148 (MQ=255)                                                                                                       tAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATAttt                                      <  1:608071/148‑1 (MQ=255)                                                                                                              acacCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCAt                               >  1:512746/1‑148 (MQ=255)                                                                                                                             ataaaAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAGGTTACGTTGTGCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCatta                >  1:28004/1‑148 (MQ=255)                                                                                                                             ataaaAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCatta                >  1:517214/1‑148 (MQ=255)                                                                                                                                 aaGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGa            >  1:568043/1‑148 (MQ=255)                                                                                                                                  agagGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCCTCATTATTGAt           >  1:241517/1‑148 (MQ=255)                                                                                                                                  agagGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGGTCGATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGAt           >  1:122125/1‑148 (MQ=255)                                                                                                                                       aggCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGATTTCAt      >  1:227709/1‑148 (MQ=255)                                                                                                                                           cTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACCACATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGATTTCATgtgt  <  1:461575/148‑1 (MQ=255)                                                                                                                                           cTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGATTTCATgtgt  <  1:583029/148‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                 ATATGGAAACTCACCTAAAGCATATTTAGTTGTACCTATTGTTGGTGCATTCTTAATCGATTTAATTGGTGTTATAGTCATTATGGGATTCATACAATGGTTTAGTTAAACACCAAACTCATAAATAAAAGAGGAGGCCTTCGCCTCCTCTTTTATTTATCCTCGATGTATATTCAAGTTACGTTGTTCTATCCATGACAATATTTCCGGACTAAATACGATTTGTTTTTGTGTTAAGTCGTCAATATTTTTAGCATCTAACATCGTCATTATTGATTTCATGTGT  >  USA300TCH1516_ALE/2464596‑2464881

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