New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2067939	221 (1.080)	14 (0.080)	8/138	NT	6.1%	intergenic (+52/‑368)	ppaC/mdlD	putative manganese‑dependent inorganic pyrophosphatase/NAD(P)‑dependent benzaldehyde dehydrogenase
	?	USA300TCH1516_ALE	= 2067962	239 (1.360)					intergenic (+75/‑345)	ppaC/mdlD	putative manganese‑dependent inorganic pyrophosphatase/NAD(P)‑dependent benzaldehyde dehydrogenase

TCGAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2067839‑2067939 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacagttcattGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  USA300TCH1516_ALE/2067962‑2067873                                                                                                                                                                                                 TCGAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTA                                                                                                      <  2:2121017/91‑1  CGAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAA                                                                                                     <  1:1752406/91‑1  CGAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAA                                                                                                     >  1:2073583/1‑91  CGAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAA                                                                                                     <  1:571245/91‑1   GAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAAC                                                                                                    <  1:705118/91‑1     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  >  1:1433078/1‑91     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  <  2:3243915/91‑1     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  <  2:3201931/91‑1     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  >  2:1952179/1‑91     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  >  2:1952099/1‑91     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  <  2:1782806/91‑1     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  <  2:1493633/91‑1     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  >  1:2639457/1‑91     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  <  1:2633370/91‑1     AAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  >  1:1990378/1‑91     AAAAAACAAAACATACCTCAAATCTCTGAAGCATTATCAAAATAATACTATATTACTGTATAATTATAGACATGTTGTATTTAACTAACAG                                                                                                  <  2:2734426/91‑1      AAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGT                                                                                                 <  2:2759062/91‑1        AAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTC                                                                                               >  2:2818378/1‑91         AACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCA                                                                                              >  2:3269555/1‑91           CAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATT                                                                                            >  1:2269092/1‑91                            CACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTC                                                                           <  1:2550961/91‑1                            CACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTC                                                                           <  1:270951/91‑1                            CACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTC                                                                           <  1:2550582/91‑1                            CACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTC                                                                           <  1:2550388/91‑1                                GAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACT                                                                       <  1:2574084/91‑1                                  AGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTT                                                                     <  1:3183015/91‑1                                    CATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTTAA                                                                   <  2:1266007/91‑1                                       TAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGA                                                                <  2:1299169/91‑1                                         ACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAAC                                                              <  2:3406400/91‑1                                         ACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAAC                                                              <  2:377823/91‑1                                         ACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAAC                                                              <  2:2955001/91‑1                                          CAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAGCAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACT                                                             <  2:3258049/91‑1                                          CAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAGCAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACT                                                             <  2:3258050/91‑1                                             AATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTT                                                          <  1:882026/91‑1                                                                                            ACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTT           <  1:1581741/91‑1                                                                                            ACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTT           >  1:29014/1‑91                                                                                            ACAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTT           >  1:272587/1‑91                                                                                             CAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTT          <  2:3265663/91‑1                                                                                             CAGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTT          <  2:750627/91‑1                                                                                              AGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTG         <  2:1377133/91‑1                                                                                              AGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTG         <  1:3256102/91‑1                                                                                              AGTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTG         <  2:1262185/91‑1                                                                                               GTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGT        >  1:1792834/1‑91                                                                                               GTTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGT        >  1:3469395/1‑91                                                                                                TTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTT       <  2:551194/91‑1                                                                                                TTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTT       <  1:3949794/91‑1                                                                                                TTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTT       >  1:2532990/1‑91                                                                                                TTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTT       >  2:3235727/1‑91                                                                                                TTCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTT       <  1:2713499/91‑1                                                                                                 TCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTA      >  2:39832/1‑91                                                                                                 TCATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTA      <  1:126465/91‑1                                                                                                  CATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAA     >  1:2623761/1‑91                                                                                                  CATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAA     <  2:2549276/91‑1                                                                                                  CATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAA     >  1:241568/1‑91                                                                                                   ATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACTGTAATATAGTATTATTTTGTTAAT    >  2:3678713/1‑91                                                                                                   ATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTCAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAAT    >  2:3678443/1‑91                                                                                                   ATTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTCAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAAT    >  2:3678239/1‑91                                                                                                    TTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATG   <  1:2569972/91‑1                                                                                                    TTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATG   <  1:3851619/91‑1                                                                                                    TTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATG   <  1:3851784/91‑1                                                                                                    TTGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATG   <  1:1901919/91‑1                                                                                                     TGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  1:3910682/91‑1                                                                                                     TGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  >  2:290587/1‑91                                                                                                     TGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  1:2344344/91‑1                                                                                                     TGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  2:1303655/91‑1                                                                                                     TGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  1:2334999/91‑1                                                                                                     TGAAAGTGAAAGAAATTCTACTTTAATGGACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  2:1554198/91‑1                                                                                                                                                                                                 TCGAAAAAAACAAATCGTACCTCAAATCACTGAAGCATTAACAAAATAATACTATATTACTGTCTAATTATAGACATGTTGTATTTAACTAACAGTTCATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2067839‑2067939 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aacagttcattGAAAGTGAAATAAATTCTACTTTAATGAACTGTTAGTTAAATACAACATGTCTATAATTAGACAGTAATATAGTATTATTTTGTTAATGC  <  USA300TCH1516_ALE/2067962‑2067873

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.