New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2357390	155 (0.760)	10 (0.060)	9/140	NT	6.5%	intergenic (‑340/+198)	ecfA1/rplQ	Energy‑coupling factor transporter ATP‑binding protein EcfA1/50S ribosomal protein L17
	?	USA300TCH1516_ALE	= 2357406	152 (0.850)					intergenic (‑356/+182)	ecfA1/rplQ	Energy‑coupling factor transporter ATP‑binding protein EcfA1/50S ribosomal protein L17

ATACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2357291‑2357390 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcggacttaTGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTT  <  USA300TCH1516_ALE/2357406‑2357318                                                                                                                                                                                               ATACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAA                                                                                                    >  2:2609947/1‑91   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  >  2:2499325/1‑91   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  >  1:1888521/1‑91   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  >  1:1888987/1‑91   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  >  1:2678596/1‑91   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  <  2:2791096/91‑1   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  >  1:2638818/1‑91   ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                  >  1:2638694/1‑91    CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                 >  1:3917208/1‑91    CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                 <  1:3643790/91‑1    CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                 <  2:532923/91‑1    CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                 <  1:2238624/91‑1    CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                 <  1:2238733/91‑1    CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                 >  1:2279387/1‑91       TCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGAC                                                                                              <  2:2411599/91‑1        CACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACT                                                                                             <  1:1128913/91‑1        CACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACT                                                                                             <  1:1135246/91‑1          CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                           <  1:2257035/91‑1                       TAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGT                                                                              <  2:522090/91‑1                         GTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTT                                                                            <  1:102255/91‑1                          TGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTT                                                                           <  2:223708/91‑1                           GAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTT                                                                          <  1:11587/91‑1                           GAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTT                                                                          <  2:1582434/91‑1                               TTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGT                                                                      <  1:3215040/91‑1                                TGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTC                                                                     <  1:3754134/91‑1                                 GATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCC                                                                    <  2:1460562/91‑1                                             TTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATA                                                        <  1:3627798/91‑1                                                      TTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTT                                               >  2:689994/1‑91                                                                                           ATCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTG          >  1:3715659/1‑91                                                                                           ATCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTG          <  1:914685/91‑1                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGTGTGCTAATCTAAAAATATGATGAAGCTAGTTTGt         >  2:1585751/1‑90                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         <  2:1714234/91‑1                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         <  2:1332130/91‑1                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         <  2:2745350/91‑1                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         >  1:2155910/1‑91                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         >  1:57722/1‑91                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         <  1:3934071/91‑1                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         <  1:3096227/91‑1                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         >  1:1718117/1‑91                                                                                            TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA         <  2:1332796/91‑1                                                                                             CGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGAT        <  2:3181632/91‑1                                                                                             CGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGAT        >  1:3648184/1‑91                                                                                             CGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGAT        >  2:2146537/1‑91                                                                                             CGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGAT        >  1:1483756/1‑91                                                                                             CGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGAT        <  1:1984994/91‑1                                                                                              GGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATC       <  2:3586518/91‑1                                                                                              GGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATC       <  2:2902389/91‑1                                                                                              GGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATC       <  1:2051407/91‑1                                                                                               GACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCA      <  2:92591/91‑1                                                                                               GACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCA      <  2:1156573/91‑1                                                                                               GACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCA      <  2:1440850/91‑1                                                                                               GACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCA      <  2:92251/91‑1                                                                                                ACTTATGAACAGTAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA     >  1:3048654/1‑91                                                                                                ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTTTTTTCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA     >  2:3105168/1‑91                                                                                                ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA     >  1:3048527/1‑91                                                                                                ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA     >  2:1480775/1‑91                                                                                                 CTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAAT    >  2:659461/1‑91                                                                                                 CTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAAT    >  2:252153/1‑91                                                                                                 CTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAAT    >  1:2374516/1‑91                                                                                                 CTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAAT    >  2:1406212/1‑91                                                                                                 CTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAAT    >  2:1406124/1‑91                                                                                                  TTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATT   <  2:338843/91‑1                                                                                                  TTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATT   <  2:338814/91‑1                                                                                                   TATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTT  >  2:2352674/1‑91                                                                                                   TATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTAACTTTTTTGAGTGCGAATCTAACAATTTAATAAAGCTAGTTTGATCAATTT  >  2:2353456/1‑91                                                                                                   TATGAACAGAAATGCTTTTAAGTCCGCTTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTT  >  2:2352729/1‑91                                                                                                                                                                                               ATACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2357291‑2357390 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcggacttaTGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTT  <  USA300TCH1516_ALE/2357406‑2357318

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.