New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 481452 =1 (0.020)54 (1.180) 36/242 0.2 98.2% coding (236/648 nt) acrR multidrug efflux transporter transcriptional repressor AcrR
?NZ_CP009273 = 3577554 NA (NA)intergenic (+14/‑210) BW25113_RS17830/BW25113_RS25760 IS1‑like element IS1A family transposase/hypothetical protein

CCATTTCTCCGACAAATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/481586‑481452
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG  <  NZ_CP009273/3577554‑3577418
                                                                                                                                                                                                                                                                                
CCATTTCTCCGACAAATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAA                                                                                                                                       <  2:48326/139‑1
     TCTCCGACAAATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACT                                                                                                                                  >  2:174904/1‑139
         CGACAAATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAA                                                                                                                              >  1:116147/1‑139
         CGACAAATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCC                                                                                                                                <  2:432295/137‑1
          GACAAATTCGCATTTGTGGAATATAATCTTCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAAC                                                                                                                             >  1:641964/1‑139
               ATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATT                                                                                                                        <  2:602057/139‑1
                   GCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATA                                                                                                                    <  1:471245/139‑1
                          TGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTT                                                                                                             <  2:537212/139‑1
                               TATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                        >  1:658136/1‑139
                               TATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                        <  2:166609/139‑1
                                    TCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGA                                                                                                    >  1:625565/1‑138
                                    TCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGA                                                                                                    >  1:74790/1‑138
                                       CCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCC                                                                                                                                >  1:284564/1‑107
                                       CCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCC                                                                                                                                <  2:284564/107‑1
                                         ATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGC                                                                                              >  2:329791/1‑139
                                           CAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                                                                                            >  1:699377/1‑139
                                             ATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGA                                                                                          <  2:699377/139‑1
                                                  CGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACT                                                                                     >  2:83466/1‑139
                                                        CGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCA                                                                               <  1:598948/139‑1
                                                                  TCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACT                                                                                                                                  >  2:820591/1‑78
                                                                  TCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACT                                                                                                                                  <  1:820591/78‑1
                                                                                      TGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGC                                                 <  1:250068/139‑1
                                                                                      TGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCA                                                                               >  1:690662/1‑109
                                                                                      TGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCA                                                                               <  2:690662/109‑1
                                                                                                    TCTTAATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAG                                   >  1:435853/1‑139
                                                                                                        AATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGGCCCAGCC                                 <  1:472806/137‑1
                                                                                                         ATACTGAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTG                              <  2:72238/139‑1
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGCCTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  1:588523/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  1:348480/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  2:667591/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  2:656422/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  2:587480/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  1:31961/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  1:693458/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  1:741500/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGG                         >  1:822847/1‑139
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGC                                                 <  1:581167/115‑1
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGC                                                 >  2:581167/1‑115
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                        <  2:325254/60‑1
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                                        >  1:325254/1‑60
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGAT                                                                                                                     <  2:808423/47‑1
                                                                                                              GAGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGAT                                                                                                                     >  1:808423/1‑47
                                                                                                               AGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAA                                                                                                                              >  1:218359/1‑37
                                                                                                               AGAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAA                                                                                                                              <  2:218359/37‑1
                                                                                                                GAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTG                       >  2:831360/1‑139
                                                                                                                GAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATT                                                               >  2:408794/1‑99
                                                                                                                GAGTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATT                                                               <  1:408794/99‑1
                                                                                                                  GTGGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCT                     <  2:741500/139‑1
                                                                                                                    GGATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGC                   >  1:756798/1‑139
                                                                                                                     GATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCC                  >  2:168097/1‑139
                                                                                                                      ATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCT                 <  1:329791/139‑1
                                                                                                                      ATCGCCAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCT                 >  1:267317/1‑139
                                                                                                                           CAGGGAATTTTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGAT            <  2:435853/139‑1
                                                                                                                                     TGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG  >  1:202239/1‑139
                                                                                                                                      GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG  <  1:831360/138‑1
                                                                                                                                                                                                                                                                                
CCATTTCTCCGACAAATTCGCATTTGTGGAATATAATCTCCATCAATAATCGACGCCGTTCTTCTGTCACCGTGGATTCAAGAACATGAATTAATATCTCTCTTAATACTGAGAGTGGATCGCCAGGGAATTTTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NZ_CP009273/481586‑481452
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATTCAGGTTATG  <  NZ_CP009273/3577554‑3577418

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ 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.