New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 3666120 =132 (1.070)19 (0.190) 7/148 NT 15.8% intergenic (‑310/+60) gadX/gadA acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent
?NC_000913 3666163 = 93 (0.910)intergenic (‑353/+17) gadX/gadA acid resistance regulon transcriptional activator; autoactivator/glutamate decarboxylase A, PLP‑dependent

GATCACCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3666233‑3666120
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gctgggcattcggttTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  >  NC_000913/3666163‑3666261
                                                                                                                                                                                                                     
GATCACCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAG                                                                                                                   >  1:1442067/1‑100
  TCACCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCT                                                                                                                 >  2:1981490/1‑100
   CACCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCT                                                                                                                 <  1:2269650/99‑1
    ACCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGG                                                                                                               <  2:3030606/100‑1
     caCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              >  2:2286694/3‑100
     CCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              >  1:3388377/1‑100
     CCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              >  2:879303/1‑100
     CCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              >  2:775400/1‑100
     CCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              <  2:3262871/100‑1
     CCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              >  2:154908/1‑100
     CCCGAAACTGCAGGGTATTGACCAGCAGAACAGCGTTAAACACACCTGATAACAGAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGG                                                                                                              <  1:106501/100‑1
      CCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGC                                                                                                             >  2:523672/1‑100
       CGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCA                                                                                                            >  2:1145495/1‑100
          AACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTC                                                                                                         >  2:320456/1‑100
          AACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGAACAGCCTTTAAAAAAACAGCTGGGCATTC                                                                                                         <  1:3353756/100‑1
            CTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGG                                                                                                       <  2:1388006/100‑1
            CTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGG                                                                                                       >  2:1282582/1‑100
            CTGCAGGGTATTGACCAGCAGACCAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGACTGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGG                                                                                                       <  1:2515949/100‑1
              GCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTT                                                                                                     >  1:1293261/1‑100
                          CCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTA                                                                                         >  2:3078603/1‑100
                                                        ACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGC                                                           >  2:1468507/1‑100
                                                                         CCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAG                                          >  1:2045577/1‑100
                                                                         CCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAG                                          >  2:3072696/1‑100
                                                                         CCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAG                                          >  2:2536925/1‑100
                                                                         CCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAG                                          >  1:1884777/1‑100
                                                                         CCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGGGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAG                                          >  2:2381943/1‑100
                                                                         CCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTGTTACAACGTTATGTTATCAGGTGTGTGTAAAGCTGTTCTGCTGGTCAATACCCTGCAG                                          >  2:998655/1‑100
                                                                         CCGAACGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTCTCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGC                                            >  2:2093000/1‑98
                                                                          CGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGT                                         >  1:3079663/1‑100
                                                                           GAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTT                                        >  2:1531591/1‑100
                                                                           GAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGATTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACGCTGCAGTT                                        >  1:2011748/1‑100
                                                                             ATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTC                                      >  2:360869/1‑100
                                                                             ATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTT                                       >  1:1708656/1‑99
                                                                               GCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTag                                     >  2:1792181/1‑97
                                                                               GCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGG                                    >  2:1015223/1‑100
                                                                               GCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGG                                    >  2:734494/1‑100
                                                                               GCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGG                                    >  2:429352/1‑100
                                                                               GCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGG                                    >  2:2494922/1‑100
                                                                                                   GCTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTC                 >  1:2302008/1‑99
                                                                                                    CTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAG               <  1:932576/100‑1
                                                                                                    CTGGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAG               >  1:1779554/1‑100
                                                                                                      GGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGG             >  1:25436/1‑100
                                                                                                      GGGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGG             >  2:159507/1‑100
                                                                                                       GGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGA            <  2:673658/100‑1
                                                                                                       GGCATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGA            >  2:1559748/1‑100
                                                                                                          ATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGC         <  1:1743028/100‑1
                                                                                                          ATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGC         >  1:1918339/1‑100
                                                                                                          ATTCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGC         >  2:1783297/1‑100
                                                                                                            TCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTT       <  2:2202417/100‑1
                                                                                                            TCGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTT       >  2:506179/1‑100
                                                                                                             CGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTT      >  1:2748150/1‑100
                                                                                                             CGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTT      <  2:3191105/100‑1
                                                                                                             CGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTT      >  1:2037781/1‑100
                                                                                                             CGGTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTT      >  2:2127465/1‑100
                                                                                                              GGTTTTTACAACGTTAGGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTGTG     >  2:2019598/1‑100
                                                                                                               GTTTTTACAACGTTCTGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCTCTGAGATATTTCAGGGAGGCTTTGT    >  1:2402054/1‑100
                                                                                                               GTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGT    >  2:1337362/1‑100
                                                                                                               GTTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGT    <  1:1337357/100‑1
                                                                                                                TTTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTA   <  2:1811615/100‑1
                                                                                                                 TTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCTGGTGATCGCCGAGATATTTCAGGGAGGCTTTGTAG  >  1:1861295/1‑100
                                                                                                                 TTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  <  2:1877250/100‑1
                                                                                                                 TTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  <  1:2933592/100‑1
                                                                                                                 TTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  <  2:1209169/100‑1
                                                                                                                 TTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  <  2:1388023/100‑1
                                                                                                                 TTTTACAACGTTATGTAATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  <  1:1137654/100‑1
                                                                                                                                                                                                                     
GATCACCCGAAACTGCAGGGTATTGCCCAGCAGAACAGCTTTAAACACACCTGATAACATAACGTTGTAAAAACCGAATGCCCAGCCTTTAAAAAAACAGCTGGGCATTCGGTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/3666233‑3666120
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gctgggcattcggttTTTACAACGTTATGTTATCAGGTGTGTTTAAAGCTGTTCTGCTGGGCAATACCCTGCAGTTTCGGGTGATCGCTGAGATATTTCAGGGAGGCTTTGTAG  >  NC_000913/3666163‑3666261

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