New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3653230	NA (NA)	48 (0.960)	36/276	0.3	96.0%	noncoding (1/1195 nt)	IS5	repeat region
	?	NC_000913	= 3766089	2 (0.040)					coding (3907/4134 nt)	rhsA	rhs element protein RhsA

CTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAA  >  NC_000913/3653099‑3653365                                                                                                                                    |                                                                                                                                        ctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGa                                                                                                                                 <  2:594650/140‑1 (MQ=31)   tttCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGaca                                                                                                                               <  1:339697/140‑1 (MQ=33)      cTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTa                                                                                                                            <  2:546846/140‑1 (MQ=34)             gACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttttt                                                                                                                     <  2:493182/140‑1 (MQ=40)              aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGacac                                                                                                                              <  2:364894/130‑1 (MQ=34)              aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGacac                                                                                                                              >  1:364894/1‑130 (MQ=33)              aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTa                                                                                                                    >  1:169649/1‑140 (MQ=255)              aCGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTa                                                                                                                    >  2:159673/1‑140 (MQ=255)                ggCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACa                                                                                                                  <  1:510591/140‑1 (MQ=255)                 gcgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACAt                                                                                                                 <  2:214085/140‑1 (MQ=255)                   gcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAtttt                                                                                                                        >  1:649370/1‑131 (MQ=38)                   gcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAtttt                                                                                                                        <  2:649370/131‑1 (MQ=39)                   gcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGATGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATaa                                                                                                               >  2:762597/1‑140 (MQ=255)                       aCTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGaa                                                                                                           >  2:385541/1‑140 (MQ=255)                        ctgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttttt                                                                                                                     >  1:535901/1‑129 (MQ=255)                        ctgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTAttttttt                                                                                                                     <  2:535901/129‑1 (MQ=255)                            tgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACAccc                                                                                                      <  2:169649/140‑1 (MQ=255)                              aaTTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTa                                                                                                    <  2:296271/140‑1 (MQ=255)                                   aCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccccc                                                                                               <  2:6371/140‑1 (MQ=255)                                   aCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTAccccc                                                                                               <  1:347023/140‑1 (MQ=255)                                    cTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCa                                                                                              <  2:490111/140‑1 (MQ=255)                                     tGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCaa                                                                                             >  1:14419/1‑140 (MQ=255)                                     tGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCaa                                                                                             <  1:762597/140‑1 (MQ=255)                                      gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCaaa                                                                                            <  1:385541/140‑1 (MQ=255)                                                 caaattGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGa                                                                                 <  1:291839/136‑1 (MQ=255)                                                      tgatgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGAc                                                                            <  1:384555/140‑1 (MQ=255)                                                             tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCt                                                                     >  2:698226/1‑140 (MQ=255)                                                               atgatgAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTg                                                                   >  1:124316/1‑140 (MQ=255)                                                                    gaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGacaaa                                                              <  1:568400/140‑1 (MQ=255)                                                                       cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGacaaacaa                                                           >  1:346079/1‑140 (MQ=255)                                                                           gTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCg                                                       <  1:588956/140‑1 (MQ=255)                                                                            ttCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGa                                                      >  1:499616/1‑140 (MQ=255)                                                                                     tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAtt                                             <  2:14419/140‑1 (MQ=255)                                                                                     tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAtt                                             <  2:499616/140‑1 (MQ=255)                                                                                      ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAttt                                            >  2:80056/1‑140 (MQ=255)                                                                                      ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAttt                                            >  2:8782/1‑140 (MQ=255)                                                                                      ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAttt                                            >  2:122664/1‑140 (MQ=255)                                                                                      ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAttt                                            >  1:53517/1‑140 (MQ=255)                                                                                      ccAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTAttt                                            <  1:434736/140‑1 (MQ=255)                                                                                              cAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGttt                                                >  1:62017/1‑128 (MQ=255)                                                                                              cAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGttt                                                <  2:62017/128‑1 (MQ=255)                                                                                                aaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACattat                                  <  1:10593/140‑1 (MQ=255)                                                                                                 aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACattatt                                 >  2:122073/1‑140 (MQ=255)                                                                                                 aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACattatt                                 <  1:8782/140‑1 (MQ=255)                                                                                                  cATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACAttatta                                <  1:159673/140‑1 (MQ=255)                                                                                                   aTGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTaa                               <  1:698226/140‑1 (MQ=255)                                                                                                             atCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGa                     >  2:634188/1‑140 (MQ=255)                                                                                                              tCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGAc                    <  2:346079/140‑1 (MQ=255)                                                                                                                 gggACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAAc                 >  1:555411/1‑140 (MQ=255)                                                                                                                  ggACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAAcc                >  2:262448/1‑140 (MQ=255)                                                                                                                     cTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCttt             >  1:236302/1‑140 (MQ=255)                                                                                                                         ttCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACg         >  2:60175/1‑140 (MQ=255)                                                                                                                                cttccttAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCaaaa  >  1:398919/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                        CTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAGGTGACACTATTTTTTTACATAAAGAACACCCTACCCCCAAATTATATAAAGATGGACAATATCTTGACAAACAAATCGAAGGTTTATTTTCAACATTATTAACCATTAATGACAACCTTTTACGAGCAAAA  >  NC_000913/3653099‑3653365

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