New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2665491	149 (0.730)	19 (0.110)	11/138	NT	13.0%	intergenic (‑118/+61)	USA300TCH1516_02535/sdhA	hypothetical protein/L‑serine dehydratase, alpha chain
	?	USA300TCH1516_ALE	= 2665513	125 (0.710)					intergenic (‑140/+39)	USA300TCH1516_02535/sdhA	hypothetical protein/L‑serine dehydratase, alpha chain

GTTATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2665391‑2665491 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagaagcatctGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGTG  <  USA300TCH1516_ALE/2665513‑2665424                                                                                                                                                                                                 GTTATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTA                                                                                                      >  1:3073808/1‑91 GTTATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTA                                                                                                      >  1:1608490/1‑91   TATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAG                                                                                                    >  2:2558918/1‑91    ATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGA                                                                                                   <  2:3889231/91‑1    ATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGA                                                                                                   >  1:1893421/1‑91     TTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAA                                                                                                  >  1:488493/1‑91      TTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAG                                                                                                 >  1:1996305/1‑91      TTTAGATAGACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAG                                                                                                 <  2:2228024/91‑1       TTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGC                                                                                                >  2:2493335/1‑91       TTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGC                                                                                                >  2:627672/1‑91       TTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGC                                                                                                >  2:627900/1‑91       TTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGC                                                                                                <  1:2289386/91‑1       TTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGC                                                                                                <  1:2289761/91‑1       TTAGATATACGGGGGAGCTTCTGCAATCACCATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGCTACTTACGAAGC                                                                                                >  2:2493718/1‑91         AGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCAT                                                                                              >  2:2732424/1‑91         AGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCAT                                                                                              >  1:2041238/1‑91          GATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATC                                                                                             >  2:1876751/1‑91          GATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATC                                                                                             <  2:615200/91‑1           ATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT                                                                                            <  1:2371892/91‑1           ATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT                                                                                            >  2:2674900/1‑91           ATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT                                                                                            <  2:2807647/91‑1           ATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT                                                                                            >  1:311205/1‑91           ATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT                                                                                            >  2:3327243/1‑91                   GGGCGCTTTTGTAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGAT                                                                                    <  1:3579568/91‑1                               AATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAG                                                                        <  1:1117292/91‑1                                ATCACCATTTTGATTAGTATGCA‑TTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGAT                                                                      <  1:2887786/91‑1                                 TCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGAT                                                                      <  1:1259959/91‑1                                 TCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGAT                                                                      <  2:2681384/91‑1                                 TCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCCGGATCATTAGTACCAGAT                                                                      <  2:3483656/91‑1                                   ACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAG                                                                    <  2:153290/91‑1                                    CTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGA                                                                   <  2:1428796/91‑1                                    CTATTTTGATTAGTATGCATTTTCCATAAATCTATCAACTTCTTCAGAGATAATTAAGATGCATCTGTCTGGATCATTAGTACCAGATAGA                                                                   <  1:3512449/91‑1                                     TATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGAT                                                                  <  1:1626670/91‑1                                     TATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGAT                                                                  <  1:295497/91‑1                                     TATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGAT                                                                  <  2:2904833/91‑1                                     TATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAAAAAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGAT                                                                  <  1:1280490/91‑1                                      ATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATG                                                                 <  1:267754/91‑1                                      ATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATG                                                                 <  1:267849/91‑1                                           GATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGCAGCACCTGTCTGGATCATTAGTACCAGATAGATGCTTCT                                                            <  1:2743594/91‑1                                             TTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTA                                                          <  1:760511/91‑1                                              TAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAAAAAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAA                                                         <  1:1784453/91‑1                                                                 ATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGA                                      <  2:3518792/91‑1                                                                                           AAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAAT            <  2:875781/91‑1                                                                                           AAGAAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAAT            >  2:3241459/1‑91                                                                                           AAGAAGCATCTGTCTGGATCATTAGTACCAGATAGACGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAAT            <  2:3117953/91‑1                                                                                            AGAAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATC           >  1:3629566/1‑91                                                                                            AGAAGCATCTGTCTGGATCAGTAGTACCAGATAGATGCTTCTTAATTATCTCCGAAGCAGTTGAAAGATTTATGGAAAATGCATACTAATC           >  2:78734/1‑91                                                                                              AAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAA         <  2:2755012/91‑1                                                                                              AAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAA         >  1:497679/1‑91                                                                                              AAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAA         <  2:2754429/91‑1                                                                                              AAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAA         >  1:1159937/1‑91                                                                                              AAGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAA         <  2:3388152/91‑1                                                                                              AAGCATCTGTCTGGATCATGAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAA         <  2:3387727/91‑1                                                                                              AAGCATCTGTCTGGATCATCAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATCTATGGAAAATGCATACTAATCAA         >  2:1777898/1‑91                                                                                               AGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAA        >  2:2682739/1‑91                                                                                               AGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAA        >  1:2390551/1‑91                                                                                               AGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAA        >  1:454180/1‑91                                                                                               AGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAA        <  2:1887663/91‑1                                                                                               AGCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAA        >  2:3111129/1‑91                                                                                                tCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAA       >  2:2860432/2‑91                                                                                                GCATCTGTCTGGATCATTAGTACCAGATATATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAA       <  1:3171529/91‑1                                                                                                GCATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAA       <  2:241770/91‑1                                                                                                 CATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAAT      >  1:1123169/1‑91                                                                                                 CATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAAT      <  2:350630/91‑1                                                                                                 CATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAAT      <  2:1226930/91‑1                                                                                                 CATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAAT      >  2:189714/1‑91                                                                                                 CATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAAGGCATACTAATCAAAAT      <  2:3168797/91‑1                                                                                                  ATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATA     >  1:2774500/1‑91                                                                                                  ATCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATA     >  2:211783/1‑91                                                                                                   TCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAG    <  2:2871659/91‑1                                                                                                   TCTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAG    >  1:2083020/1‑91                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAAaaaa   <  2:2700226/91‑5                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGT   <  2:1585853/91‑1                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGT   <  1:3594323/91‑1                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGT   >  1:3494446/1‑91                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGT   <  2:2819637/91‑1                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGT   >  1:3494445/1‑91                                                                                                    CTGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGT   <  1:1706575/91‑1                                                                                                     TGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGTG  <  2:1835058/91‑1                                                                                                     TGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGTG  >  2:3408357/1‑91                                                                                                     TGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGTG  >  2:786170/1‑91                                                                                                                                                                                                 GTTATTTTAGATATACGGGGGCGCTTTTGCAATCACTATTTTGATTAGTATGCATTTTCCATAAATCTTTCAACTTCTTCAGAGATAATTAAGAAGCATCT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2665391‑2665491 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagaagcatctGTCTGGATCATTAGTACCAGATAGATGCTTCTTAATTATCTCTGAAGAAGTTGAAAGATTTATGGAAAATGCATACTAATCAAAATAGTG  <  USA300TCH1516_ALE/2665513‑2665424

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