New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_pgi = 3584195NA (NA)20 (0.380) 18/270 NT 37.7% intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E
?NC_000913_3_pae_pgi = 3665158 33 (0.620)coding (653/825 nt) gadX acid resistance regulon transcriptional activator; autoactivator

CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/3584063‑3584195
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACT  <  NC_000913_3_pae_pgi/3665158‑3665016
                                                                                                                                                                                                                                                                                    
CCTGAATCTGATGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTAAAAATCGTTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTA                                                                                                                                 <  1:326219/149‑1
 CTGAATCTGAGGCAGCACTTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTAT                                                                                                                                <  1:22025/149‑1
 CTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGGCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGGCATTACCATCACAGCGTGTCGTAT                                                                                                                                >  2:6749/1‑149
         GAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTA                                                                                                                        <  2:496541/149‑1
                CACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTCCATATAACCGGGTGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTT                                                                                                                 <  1:779525/149‑1
                          GGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGCCAAAGTCATCGGGCATTATCTGAACATAAAACACTATAAATAAGTTGGAGTCATTACCATCAAAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATT                                                                                                       >  1:15091/1‑149
                                           CTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACA                                                                                      <  1:974471/149‑1
                                             GTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGA                                                                                    <  1:767792/149‑1
                                             GTCGTTCTCAAAATCGGGGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGA                                                                                    <  1:459640/149‑1
                                              TCGTTCTCAATATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACATCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAG                                                                                   <  2:963561/149‑1
                                              TCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTAGAATTTATTATTAGATGACGCCCACAGAG                                                                                   >  1:730657/1‑149
                                                    TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCACTAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATacg                                                                             >  1:345566/1‑146
                                                    TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAG                                                                             >  1:342062/1‑149
                                                             GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATCAGTTGGAGTCATTACCATCACGGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCG                                                                    <  2:140575/149‑1
                                                             GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTCCGTCTTTCGAAATTATTATGGGATGCCGCCCACAGAACATCACGAACGGTCG                                                                    >  2:250116/1‑149
                                                                          ACAAAGTCACCGGGCATGAGCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGT                                                       <  1:130404/149‑1
                                                                                  ATCGGGCATTATCTGAACATATAACACTCTTAATAAGTTGGGTTTATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGT                                               <  1:115667/149‑1
                                                                                      GGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGCCT                                           >  1:216908/1‑149
                                                                                                        AACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTCTTCTGGGATGCCGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTAGAAAAGTGACTCGGCGGCAAGTATTGTTG                         >  1:781916/1‑149
                                                                                                                               ATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACT  >  2:811160/1‑149
                                                                                                                                                                                                                                                                                    
CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/3584063‑3584195
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACT  <  NC_000913_3_pae_pgi/3665158‑3665016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.