New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_pae_tpiA 164559 =47 (1.210)4 (0.110) 4/268 5.1 9.6% intergenic (+25/‑171) hrpB/mrcB putative ATP‑dependent helicase/fused glycosyl transferase and transpeptidase
?NC_000913_3_pae_tpiA 289255 = 31 (0.850)intergenic (‑93/+46) yagI/argF CP4‑6 prophage; putative DNA‑binding transcriptional regulator/ornithine carbamoyltransferase 2, chain F; CP4‑6 prophage
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GACTTCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTT  >  NC_000913_3_pae_tpiA/164412‑164702
                                                                                                                                                   |                                                                                                                                                
gACTTCTGGAAAGGAGGGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGGCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTgg                                                                                                                                                 <  1:143398/149‑1 (MQ=255)
   ttCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGCAATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGgag                                                                                                                                              >  2:634369/1‑149 (MQ=255)
   ttCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAACGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGgag                                                                                                                                              >  1:181302/1‑149 (MQ=255)
     cTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTTAGGTTGGTTTTCTCCCTCTCCCTGTGGGagag                                                                                                                                            >  1:26183/1‑149 (MQ=255)
      tGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAgg                                                                                                                                           >  1:73280/1‑149 (MQ=255)
         aaaGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCTTAAGGTTGGTTTTCGCCCTCTCCCACAGGGAGAgggag                                                                                                                                        <  2:147668/149‑3 (MQ=255)
         aaaGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGCTTTTCTCCCTCTCCCTGTGGGAGAGGGcc                                                                                                                                        >  1:586408/1‑149 (MQ=255)
          aaGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGCGCCg                                                                                                                                       >  1:292327/1‑149 (MQ=255)
                cGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAGAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGa                                                                                                                                 <  1:450306/149‑1 (MQ=255)
                    ccGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGGCGGGGTGGGGGc                                                                                                                             >  1:135140/1‑149 (MQ=255)
                     cGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGCACGGTTGCCTCTCTGCCTCTCCCTGTGGGAGAAGGCCGGGGTGAGGGCa                                                                                                                            >  1:300047/1‑149 (MQ=255)
                       tGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGCCGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATc                                                                                                                          >  2:295237/1‑149 (MQ=255)
                               aaaaaGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCa                                                                                                                 >  2:227680/1‑149 (MQ=255)
                                       aTGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtcacc                                                                                                         <  2:181302/149‑1 (MQ=255)
                                         gAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGAACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtcaccct                                                                                                       >  2:210954/1‑149 (MQ=255)
                                          aaaGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTtcaccctc                                                                                                      >  1:370289/1‑149 (MQ=255)
                                             gggCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGAGCCGGGGTGAGGGCATCAGCGCGCACGTtcaccctcacc                                                                                                   >  1:284146/1‑149 (MQ=255)
                                                 gTTATCGTAAACACGTCGCGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTaa                                                                                               <  2:241966/149‑1 (MQ=38)
                                                      cccAAACATGTCTGGGCGGACGTCCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGCGTGAAAAAGCAGATCGGTAGTTTCACCCTCACCCTAACCctc                                                                                          <  2:490899/149‑1 (MQ=255)
                                                       ccAAACATGTCTGGCCGGGCGACCCGGCAAATACTGAAAAGAAGCGACGGACGAAAACGTGATCGAAACGTTGTTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCctct                                                                                         >  2:656008/1‑149 (MQ=25)
                                                          aaCATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTccc                                                                                      >  2:146170/1‑149 (MQ=255)
                                                                tCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAgg                                                                                >  1:228963/1‑149 (MQ=255)
                                                                tCTGGCCGGACGACCCGGCAAATACAGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTATCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGTCATCCGCGCGCACGTTCACCCCCACCCTCACCCTCTcccccccgg                                                                                >  2:51158/1‑143 (MQ=38)
                                                                  tGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCCCTCCCCCAAGGga                                                                              >  2:416390/1‑149 (MQ=255)
                                                                    gCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCctct                                                                                         >  1:109361/1‑136 (MQ=255)
                                                                    gCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCctct                                                                                         <  2:109361/136‑1 (MQ=255)
                                                                     ccGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGagag                                                                           <  2:370289/149‑1 (MQ=255)
                                                                      cGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAgg                                                                          <  2:586408/149‑1 (MQ=255)
                                                                      cGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAgg                                                                          <  1:227680/149‑1 (MQ=255)
                                                                              ccGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGGTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTACCCCTCACCCTAACCCTCTCCCTCAAGGGAGGGGAGACCGAt                                                                  >  2:407298/1‑149 (MQ=38)
                                                                                 gCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGa                                                               <  1:611630/149‑1 (MQ=255)
                                                                                            aCCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAAtttt                                                    >  1:184090/1‑149 (MQ=255)
                                                                                                acgcgacgGAGGATAAAGTATTCGGAAGGTTGGTTTTCGCCCGCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTgaga                                                <  2:328236/149‑1 (MQ=38)
                                                                                                 cgcgacgGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCAAGAACAAATTTTgagag                                               >  1:170537/1‑149 (MQ=255)
                                                                                                           gAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGACTTAGATAGGGCAGCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCAAAAATTTTGAGAGATAtcttctt                                     >  2:624710/1‑149 (MQ=255)
                                                                                                                 gTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGTAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGTGGGGACCGATCGCGCACAAATCTTGAGAGATATCTTCTTCTGTCt                               <  1:541343/149‑1 (MQ=255)
                                                                                                                   aTTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTg                             <  1:146170/149‑1 (MQ=255)
                                                                                                                      cGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCGCAAATTTTGAGAGATATCTTCTTCTGTCTTGTaa                          <  2:541688/149‑1 (MQ=255)
                                                                                                                        tAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGTGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATAGCTTCTTCTGTCTTGTAACa                        <  1:546656/149‑1 (MQ=255)
                                                                                                                            gttggttTTCTCCCTCTCCCTGGCGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACagaag                    <  1:146692/149‑1 (MQ=255)
                                                                                                                               ggttTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAAc                 >  1:6397/1‑149 (MQ=255)
                                                                                                                                gttTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCCGCGCGCACGTTTACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACa                >  1:643763/1‑149 (MQ=255)
                                                                                                                                 ttttCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAg               >  1:75061/1‑149 (MQ=255)
                                                                                                                                       ccctctcccaCAGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACag                       <  1:358207/135‑1 (MQ=255)
                                                                                                                                         ctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCGTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCgg       >  1:513250/1‑149 (MQ=255)
                                                                                                                                         ctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGCAAATCgg       >  2:586606/1‑149 (MQ=255)
                                                                                                                                         ctctccctGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCgg       <  2:6397/149‑1 (MQ=255)
                                                                                                                                              cctGTCGGAGAGGGAGGGGGTGAGGGCAGCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACCAATTTTGAGAGATGTCTTCTTCTGTCTTGTAACAGAAGAACAGAGAATCGGGCgtt  >  2:593119/1‑149 (MQ=255)
                                                                                                                                                   |                                                                                                                                                
GACTTCTGGAAAGGAGCGTACCGTGAGGTGCAAAAAGAGATGAAAGGGCGTTATCCCAAACATGTCTGGCCGGACGACCCGGCAAATACTGCACCGACGCGACGGACGAAAAAGTATTCGTAAGGTTGGTTTTCTCCCTCTCCCTGTGGGAGAGGGCCGGGGTGAGGGCATCAGCGCGCACGTTCACCCTCACCCTAACCCTCTCCCTCAAGGGAGAGGGGACCGATCGAGCACAAATTTTGAGAGATATCTTCTTCTGTCTTGTAACAGAAGAACAGAAAATCGGGCTTT  >  NC_000913_3_pae_tpiA/164412‑164702

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ 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.