New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? USA300TCH1516_ALE = 2357390140 (0.730)19 (0.110) 10/140 NT 13.3% intergenic (‑340/+198) ecfA1/rplQ Energy‑coupling factor transporter ATP‑binding protein EcfA1/50S ribosomal protein L17
?USA300TCH1516_ALE = 2357406 126 (0.760)intergenic (‑356/+182) ecfA1/rplQ Energy‑coupling factor transporter ATP‑binding protein EcfA1/50S ribosomal protein L17

ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2357293‑2357390
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcggacttaTGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTTC  <  USA300TCH1516_ALE/2357406‑2357317
                                                                                                                                                                                            
ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                   >  2:2067304/1‑91
ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                   >  1:977883/1‑91
ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATC                                                                                                   >  1:228997/1‑91
 CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                  >  2:1831354/1‑91
 CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                  >  2:3478631/1‑91
 CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                  >  2:3784742/1‑91
 CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                  >  1:2485772/1‑91
 CTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCG                                                                                                  >  2:3785211/1‑91
  TTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGG                                                                                                 <  1:2098361/91‑1
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                <  2:894584/91‑1
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                >  2:304042/1‑91
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                <  2:1587520/91‑1
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                <  2:1587317/91‑1
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                <  1:858905/91‑1
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                <  1:3141558/91‑1
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                >  1:2716182/1‑91
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                >  1:2716025/1‑91
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                >  2:559680/1‑91
   TTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGA                                                                                                <  2:738603/91‑1
     CACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACT                                                                                              <  2:3285153/91‑1
     CACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACT                                                                                              <  2:1406624/91‑1
      ACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTT                                                                                             >  2:2875948/1‑91
       CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                            <  1:298238/91‑1
       CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                            <  1:1903247/91‑1
       CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                            <  1:2473085/91‑1
       CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                            <  2:166485/91‑1
       CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                            <  2:1606732/91‑1
       CTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCAATCAAAAAAGTAAATATAAAGAAATCGGACTTA                                                                                            <  2:435896/91‑1
               AGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGA                                                                                    <  2:102325/91‑1
               AGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGA                                                                                    <  2:1021537/91‑1
               AGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGA                                                                                    <  2:1395900/91‑1
                   CTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATG                                                                                <  2:3270623/91‑1
                        GAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTT                                                                           <  1:3735789/91‑1
                        GAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTT                                                                           <  1:3055197/91‑1
                         AAATTGATCAAACTAGCTTCATCATATTTTTAGATACGAACACAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTA                                                                          <  2:1687356/91‑1
                            TTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGT                                                                       <  2:3323420/91‑1
                            TTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGT                                                                       <  2:3322936/91‑1
                            TTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGT                                                                       <  2:3323226/91‑1
                            TTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGT                                                                       <  1:990123/91‑1
                            TTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGT                                                                       <  1:835753/91‑1
                              GATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCC                                                                     <  1:2682953/91‑1
                              GATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCC                                                                     <  1:3291677/91‑1
                              GATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCC                                                                     <  1:5782/91‑1
                                TCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCCGA                                                                   <  1:1314505/91‑1
                                 CAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCCGAT                                                                  <  1:2727046/91‑1
                                      TAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTT                                                             <  1:2528072/91‑1
                                                                   CAAAAAAGTAAATATAAAGAAATCGGACTTAAAAACATTTCTGTTAATAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAA                                >  2:240382/1‑91
                                                                                        ATCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTG           >  1:989669/1‑91
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          <  2:3473421/91‑1
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          <  2:3473306/91‑1
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          >  1:667900/1‑91
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          >  1:3454645/1‑91
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          >  2:456986/1‑91
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          >  1:1864289/1‑91
                                                                                         TCGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          <  2:3706210/91‑1
                                                                                         TCGGACTTACGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGCGCGAATCTAAAAATATGATGAAGCTAGTTTGA          >  1:668555/1‑91
                                                                                         TCGAACTTATAAACAGGAATGTTTTTAAGTCCGATTTCTTTATATTTACGTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGA          <  2:878403/91‑1
                                                                                          CGGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGAT         <  2:2910208/91‑1
                                                                                           GGACTTATGAACAGAAATTTTTTTAGGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATC        <  2:2805192/91‑1
                                                                                           GGACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATC        >  2:931046/1‑91
                                                                                            GACTTATGATCAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCA       <  1:3483757/91‑1
                                                                                            GACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTTAAAATATGATGAAGCTAGTTTGATCA       <  2:2215648/91‑1
                                                                                             ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA      <  2:2481913/91‑1
                                                                                             ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA      >  2:2345216/1‑91
                                                                                             ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA      <  1:2164559/91‑1
                                                                                             ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA      <  1:1629808/91‑1
                                                                                             ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA      >  1:1247077/1‑91
                                                                                             ACTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAA      >  1:1247071/1‑91
                                                                                              CTTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAAT     >  2:1285987/1‑91
                                                                                               TTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATT    <  1:987377/91‑1
                                                                                               TTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATT    <  1:804571/91‑1
                                                                                               TTATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATT    <  1:1509940/91‑1
                                                                                                 ATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTTC  >  1:947716/1‑91
                                                                                                 ATGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTTC  <  1:2666850/91‑1
                                                                                                                                                                                            
ACTTTCACTTCATTCAGTTCTAGTGAAATTGATCAAACTAGCTTCATCATATTTTTAGATTCGCACTCAAAAAAGTAAATATAAAGAAATCGGACTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2357293‑2357390
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcggacttaTGAACAGAAATGTTTTTAAGTCCGATTTCTTTATATTTACTTTTTTGAGTGCGAATCTAAAAATATGATGAAGCTAGTTTGATCAATTTC  <  USA300TCH1516_ALE/2357406‑2357317

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.