New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 52495 =29 (1.240)43 (1.850)
+T		 3/278 2.9 62.9% intergenic (+105/‑568) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator
?CP000730 = 52988 22 (0.940)intergenic (+598/‑75) USA300HOU_0043/USA300HOU_0044 hypothetical membrane protein/possible transcriptional regulator

TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/52633‑52495
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGA  <  CP000730/52988‑52932
                                                                                                                                             |                                                         
TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCTATTACTACGATGAT‑TTCAC‑ACGATGCCTCTGATTATTTCACGTG                                                          <  1:271867/141‑1
  TCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGAT                                                        >  1:470941/1‑141
   cacACGATTCCTCTGATTATTTTACGTGATTTTCGCGCGTTTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATT                                                       <  1:459298/138‑1
   CAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGGTTATTTCCCGTGATT                                                       >  1:72971/1‑141
    AAACGATTCCTCTGATTATATCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTT                                                      >  1:297472/1‑141
              TCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATT                                            >  1:313275/1‑141
                       TTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATt                                   >  1:470207/1‑140
                          ACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCGTTGATTGTTTCACGTGATTTTCACGCGATTACTAGGATGATT                                >  1:464111/1‑141
                               ATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTATTACGATGATTTCAAA                           >  1:16323/1‑141
                                TTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCCCGTGATTTTCGCGCGATTACTACGTTGATTTaacac                          >  1:226762/1‑136
                                    CGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATATACAACACGATTC‑‑CTGATTATTTCACGTGATTTTCGCGCGATTTCTAGGATGTTTTCAAACGATT                      >  1:488710/1‑141
                                     gcgccagtcCTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCCCGAGTACTACGATGATTTCATACGATTC                     <  1:315086/132‑1
                                     GCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATT                                                       <  1:242738/107‑1
                                      CGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGTTTTCAAACGATTCC                    >  1:439968/1‑141
                                      CGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCACACGATTATAAGGATGTTTTCAAACGATcgc                    >  1:425618/1‑138
                                       gccATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATCACTACGATATTTTCAAACGATTCCT                   <  1:247866/138‑1
                                        CGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTC                  >  1:67697/1‑141
                                         GATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCT                 >  1:186574/1‑141
                                              CTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCC                    <  1:410223/133‑1
                                                ACGATGA‑TTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTACTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTT         >  1:236714/1‑141
                                                     GATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATT                                            <  1:472631/102‑1
                                                      ATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTAAAACGATTCCTCTGATTATTTCACGC    >  1:455615/1‑141
                                                        TTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGA  >  1:479385/1‑141
                                                           AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGC                                                  <  1:316453/90‑1
                                                           AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTT                                                      <  1:405343/86‑1
                                                           AAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGT                                                           <  1:43482/81‑1
                                                            AACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACG                         >  1:2679/1‑114
                                                            AACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGA                                  <  1:191858/105‑1
                                                                       TGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGA                                                         <  1:329954/71‑1
                                                                                  CGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTC        <  1:441780/109‑1
                                                                                    TGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTT                                                      <  1:432164/61‑1
                                                                                     GATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTC                     <  1:190469/93‑1
                                                                                     GATTTTCGCGCAATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGA                                                         <  1:428823/57‑1
                                                                                         TTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTC                              <  1:246345/80‑1
                                                                                             CGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGAT                       >  1:39190/1‑83
                                                                                              GCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGAT                                    >  1:477522/1‑69
                                                                                                   TACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCT                 <  1:272136/83‑1
                                                                                                         GATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTAT           >  1:124739/1‑83
                                                                                                            GAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACG                         <  1:28738/66‑1
                                                                                                            GAT‑TTCAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATT                                            <  1:156769/47‑1
                                                                                                                  CAA‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCAC      >  1:29599/1‑80
                                                                                                                    A‑ACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACG                         >  1:139675/1‑59
                                                                                                                       CGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTAC                                       >  1:370579/1‑43
                                                                                                                                           CGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTC        <  1:441765/54‑1
                                                                                                                                             |                                                         
TTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGTGATTTTCGCGCGATTACTACGATGAT‑TTCAA‑ACGATTCCTCTGATTATTTCACG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP000730/52633‑52495
‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GATTTTCGCGCGATTACTACGATGATTTCAAACGATTCCTCTGATTATTTCACGCGA  <  CP000730/52988‑52932

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.