New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3653230	NA (NA)	50 (1.050)	35/276	0.3	92.6%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 3766089	4 (0.080)					coding (3907/4134 nt)	rhsA	rhs element protein RhsA

GGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGC  >  NC_000913/3653106‑3653367                                                                                                                             |                                                                                                                                          ggTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAtt                                                                                                                            >  1:332131/1‑140 (MQ=37)    cTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttt                                                                                                                         <  1:794486/140‑1 (MQ=40)       aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTa                                                                                                                      >  2:648541/1‑140 (MQ=255)       aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTa                                                                                                                      >  2:333060/1‑140 (MQ=255)       aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTa                                                                                                                      >  1:552454/1‑140 (MQ=255)        cGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTAc                                                                                                                     <  2:406992/140‑1 (MQ=255)        cGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTAc                                                                                                                     <  2:660145/140‑1 (MQ=255)        cGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTAc                                                                                                                     <  2:518818/140‑1 (MQ=255)          gcgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACAt                                                                                                                   <  2:619880/140‑1 (MQ=255)           cgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATa                                                                                                                  <  2:437799/140‑1 (MQ=255)            gcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATaa                                                                                                                 >  2:626421/1‑140 (MQ=255)                aCTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGaa                                                                                                             <  2:375433/140‑1 (MQ=255)                   gctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAacac                                                                                                          >  1:428897/1‑140 (MQ=255)                    ctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACAcc                                                                                                         <  1:766081/140‑1 (MQ=255)                          tCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccc                                                                                                   <  1:367501/140‑1 (MQ=255)                               gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTGCCCCCaaa                                                                                              <  2:259191/140‑1 (MQ=255)                               gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCaaa                                                                                              <  2:559014/140‑1 (MQ=255)                               gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCaaa                                                                                              <  1:333060/140‑1 (MQ=255)                               gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCaaa                                                                                              <  2:685457/140‑1 (MQ=255)                                 cGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAAtt                                                                                            >  2:697377/1‑140 (MQ=255)                                   gCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATtat                                                                                          >  1:251406/1‑140 (MQ=255)                                            aGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGACCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATg                                                                                 >  2:203763/1‑140 (MQ=255)                                               tgatgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGAc                                                                              <  1:103374/140‑1 (MQ=255)                                                   gaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAata                                                                          >  1:672948/1‑140 (MQ=255)                                                   gaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAata                                                                          >  1:538728/1‑140 (MQ=255)                                                                cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGacaaacaa                                                             >  2:118332/1‑140 (MQ=255)                                                                cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGacaaa                                                                >  2:487335/1‑137 (MQ=255)                                                                cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGacaaa                                                                <  1:487335/137‑1 (MQ=255)                                                                   tGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATc                                                          >  2:352623/1‑140 (MQ=255)                                                                    gTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCg                                                         <  1:180155/140‑1 (MQ=255)                                                                     ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGa                                                        <  2:332131/140‑1 (MQ=255)                                                                     ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGa                                                        <  2:552454/140‑1 (MQ=255)                                                                         aTGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGt                                                    <  1:697377/140‑1 (MQ=255)                                                                          tGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGGCACTATTTTTCTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGtt                                                   >  2:560022/1‑140 (MQ=255)                                                                          tGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGtt                                                   >  1:473302/1‑140 (MQ=255)                                                                               ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAttt                                              >  1:721334/1‑140 (MQ=255)                                                                                   aTGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCaa                                          <  2:670890/140‑1 (MQ=255)                                                                                            aTGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTaa                                 <  2:251406/140‑1 (MQ=255)                                                                                              gATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACattatt                                   >  2:361811/1‑136 (MQ=255)                                                                                              gATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACattatt                                   <  1:361811/136‑1 (MQ=255)                                                                                                    atatCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAAt                         >  2:112037/1‑140 (MQ=255)                                                                                                      atCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGa                       >  1:151439/1‑140 (MQ=255)                                                                                                         aGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTaa                                 <  1:20047/127‑1 (MQ=255)                                                                                                         aGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTaa                                 >  2:20047/1‑127 (MQ=255)                                                                                                           ggACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAAcc                  >  2:666313/1‑140 (MQ=255)                                                                                                               ttGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCtttt              >  1:256689/1‑140 (MQ=255)                                                                                                                 gTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTAc            >  1:80501/1‑140 (MQ=255)                                                                                                                      cACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCa       >  1:702609/1‑140 (MQ=255)                                                                                                                           tccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGc  >  1:679909/1‑140 (MQ=255)                                                                                                                           tccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGc  >  1:303358/1‑140 (MQ=255)                                                                                                                             |                                                                                                                                          GGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAAGC  >  NC_000913/3653106‑3653367

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ 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.