New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2041621	207 (1.020)	17 (0.100)	9/138	NT	7.7%	intergenic (‑704/+65)	dagK/gatB_2	Diacylglycerol kinase/Aspartyl/glutamyl‑tRNA(Asn/Gln) amidotransferase subunit B
	?	USA300TCH1516_ALE	= 2041645	230 (1.310)					intergenic (‑728/+41)	dagK/gatB_2	Diacylglycerol kinase/Aspartyl/glutamyl‑tRNA(Asn/Gln) amidotransferase subunit B

AATTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2041521‑2041621 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaataaaccctTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  <  USA300TCH1516_ALE/2041645‑2041556                                                                                                                                                                                                 AATTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATA                                                                                                      <  2:3371544/91‑1  ATTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAA                                                                                                     <  2:2624960/91‑1  ATTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAA                                                                                                     >  2:1460031/1‑91  ATTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAA                                                                                                     <  1:1486621/91‑1   TTAAAGCTAACGCATTGATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAA                                                                                                    <  2:3785586/91‑1   TTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAA                                                                                                    >  1:3757535/1‑91   TTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAA                                                                                                    <  2:3408101/91‑1   TTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAA                                                                                                    <  1:616808/91‑1   TTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAA                                                                                                    >  1:3757559/1‑91   TTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAA                                                                                                    >  1:3704231/1‑91     AAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATA                                                                                                  <  2:922727/91‑1     AAAGCTAACGCATTAATAAAATTAAGATTTTTACCATTAACATGTACAATGAATAAAGGGAAAAGTAATTTGACTTCTATAGATATAAATA                                                                                                  <  2:922830/91‑1      AAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAA                                                                                                 >  1:3323698/1‑91      AAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAA                                                                                                 >  1:3188821/1‑91      AAGCTAACGCATTAATAAAATTAATATATTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCAATAGGTATAAATAA                                                                                                 <  2:2990129/91‑1       AGCTAACGCATTAATAAAATTAATGTTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAA                                                                                                <  2:2262581/91‑1       AGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAA                                                                                                <  2:2263052/91‑1        GCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAAC                                                                                               <  1:3940194/91‑1        GCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAAC                                                                                               <  2:3431163/91‑1         CTAAGGCGTTAATAATAGTAATATTTTTACCATTGACATGTACAATGAATAAAGTGAAAAGTAATTTGACTTCTATAGATATAAATAAACC                                                                                              <  2:2266521/91‑1         CTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAACAGTAATTTGTCTTCTATAGATATAAATAAACC                                                                                              <  2:2266552/91‑1         CTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACC                                                                                              >  2:3270530/1‑91         CTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACC                                                                                              <  2:1247262/91‑1         CTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACC                                                                                              >  2:3268069/1‑91         CTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACC                                                                                              <  2:3501622/91‑1         CTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACC                                                                                              <  2:3691653/91‑1          TAACGCATTAATAACATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAATACTAATTTGACTTCTATACATATAAATAACCCt                                                                                             >  2:3823509/1‑90          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             >  1:1613650/1‑91          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             <  2:2663192/91‑1          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             <  2:2457505/91‑1          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             >  2:3549750/1‑91          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             <  2:3612101/91‑1          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             <  1:3877739/91‑1          TAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCC                                                                                             <  2:3612313/91‑1           AACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCT                                                                                            <  2:3264736/91‑1                            AATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGAT                                                                           <  1:2459181/91‑1                            AATATTTTTACCATGAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGAT                                                                           <  1:2459201/91‑1                              TATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGC                                                                         <  1:2590886/91‑1                              TATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGC                                                                         <  1:2605263/91‑1                              TATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGC                                                                         <  1:2590996/91‑1                               ATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCA                                                                        <  2:3061404/91‑1                               ATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCA                                                                        <  2:3061626/91‑1                               ATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCA                                                                        <  2:3946614/91‑1                               ATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCA                                                                        <  1:2335311/91‑1                                    TACCATTAACATGGACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGA                                                                   <  2:2428308/91‑1                                     ACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAG                                                                  <  2:221758/91‑1                                     ACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAG                                                                  <  1:292247/91‑1                                     ACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAG                                                                  <  2:3896008/91‑1                                      CCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACGTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAGG                                                                 <  2:278361/91‑1                                         TTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTT                                                              <  1:2458293/91‑1                                          TAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTT                                                             <  1:122847/91‑1                                                  ACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATAT                                                     <  1:1439810/91‑1                                                                                           AAATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACAT            <  1:157051/91‑1                                                                                             gtagACCCTAGATTGCTGACTTAGGGGGAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGT          <  2:1643542/87‑1                                                                                             ATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTCCTTTTAACGTTATTCATTGTACATGT          >  2:1889295/1‑91                                                                                             ATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGc          >  2:1688994/1‑90                                                                                             ATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGT          >  2:972851/1‑91                                                                                             ATAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGT          <  1:1301295/91‑1                                                                                              TAAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTT         <  1:3233805/91‑1                                                                                               AAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTA        >  2:3241226/1‑91                                                                                               AAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTA        >  2:3241225/1‑91                                                                                               AAACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTA        <  1:2787759/91‑1                                                                                                AACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAA       <  2:2438673/91‑1                                                                                                AACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAA       <  2:1845394/91‑1                                                                                                AACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAA       >  1:2600585/1‑91                                                                                                AACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAA       >  2:1372076/1‑91                                                                                                 ACCCTTGATTGCTGACTTCGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTCTTAACTTTATTCATTGTACATGTTAAT      >  2:3423508/1‑91                                                                                                 ACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAAT      >  2:1663509/1‑91                                                                                                 ACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAAT      >  1:1021691/1‑91                                                                                                 ACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAAT      >  2:2797876/1‑91                                                                                                 ACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAAT      >  1:1896357/1‑91                                                                                                 ACCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAAT      >  1:554290/1‑91                                                                                                  CCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATG     <  2:1564803/91‑1                                                                                                  CCCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATG     >  2:520113/1‑91                                                                                                   CCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGG    <  1:633251/91‑1                                                                                                   CCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGG    <  1:1764847/91‑1                                                                                                   CCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGG    <  2:3607123/91‑1                                                                                                   CCTTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGG    >  1:1515447/1‑91                                                                                                     TTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  <  2:340924/91‑1                                                                                                     TTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  <  2:864550/91‑1                                                                                                     TTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  <  2:884313/91‑1                                                                                                     TTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  <  1:2807483/91‑1                                                                                                     TTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  >  2:25083/1‑91                                                                                                                                                                                                 AATTAAAGCTAACGCATTAATAAAATTAATATTTTTACCATTAACATGTACAATGAATAAAGTTAAAAGTAATTTGACTTCTATAGATATAAATAAACCCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2041521‑2041621 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaataaaccctTGATTGCTGACTTAGATGCAATCGAGGGTTTATTTATATCTATAGAAGTCAAATTACTTTTAACTTTATTCATTGTACATGTTAATGGTA  <  USA300TCH1516_ALE/2041645‑2041556

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