New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	734728 =	NA (NA)	30 (0.220)	11/170	NT	35.5%	pseudogene (596/1521 nt)	rhsO	pseudogene, Rhs family
	?	NC_000913	734759 =	57 (0.400)					pseudogene (627/1521 nt)	rhsO	pseudogene, Rhs family

TGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCT  >  NC_000913/734630‑734777                                                                                                   |                                                  tGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCccg                                                  >  2:2716785/1‑100 (MQ=33)   aaaCCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCccgcc                                                <  1:3171729/100‑1 (MQ=33)     aCCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCgg                                              >  2:1362843/1‑100 (MQ=32)     aCCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCgg                                              <  1:2845616/100‑1 (MQ=33)     aCCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCgg                                              >  1:2086461/1‑100 (MQ=33)      ccGCCACCGGTGAGCTGGCGTAAACGCAGCGCCGCCGACTGGCGGTTTCCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCTGTGTGGTGTTCCCGCCgg                                              >  2:3133379/1‑99 (MQ=11)      ccGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCgg                                              <  2:362646/99‑1 (MQ=32)      ccGCCACCGGTGAGCTGGCGAAAACGCAGCACCCCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGATCCCGCCGGt                                             >  2:2599685/1‑100 (MQ=255)       cGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTg                                            <  2:42086/100‑1 (MQ=33)         ccACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCt                                          <  1:991115/100‑1 (MQ=33)          cACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTAGCAGTGTGGTGTTCCCGCCGGTGCTg                                         >  1:1565259/1‑100 (MQ=17)           aCCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTgg                                        <  2:468996/100‑1 (MQ=33)           aCCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTgg                                        <  2:2135899/100‑1 (MQ=33)               gggAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCa                                    <  1:2216098/98‑1 (MQ=17)               gTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCa                                    <  1:950804/100‑1 (MQ=32)               gTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCa                                    <  1:487701/100‑1 (MQ=33)                  aGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCGTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGAt                                 <  2:3771354/100‑1 (MQ=17)                   gCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATg                                >  2:677245/1‑100 (MQ=33)                   gCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATg                                >  2:765064/1‑100 (MQ=33)                    cTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGc                               <  1:1138489/100‑1 (MQ=33)                    cTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGc                               >  2:2057188/1‑100 (MQ=32)                    cTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGc                               >  2:732459/1‑100 (MQ=32)                     tGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCt                              >  1:1083705/1‑100 (MQ=33)                      ggCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTc                             >  2:3154297/1‑100 (MQ=33)                       gCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCg                            >  1:695506/1‑100 (MQ=33)                        cGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGa                           >  1:3569953/1‑100 (MQ=33)                        cGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGa                           >  2:1718507/1‑100 (MQ=33)                        cGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGa                           >  1:1332662/1‑100 (MQ=32)                        cGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCACCGGTGCTGGTGCAGATGCTCGa                           <  2:580169/100‑1 (MQ=17)                         gAAAGCGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGAc                          <  2:1932026/100‑1 (MQ=17)                           aaaCGCAGCGCCGCAGCCTTGCGGATACCCGTCAGCAGTCCGGCGGCCAAGACGGTCGCAGTGTGGTGTTCTGTCCGGTGCTAGCGCAGATGCTCGACCg                        <  2:2163579/100‑1 (MQ=11)                              cGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCggat                     >  2:2384259/1‑98 (MQ=18)                              cGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCt                     >  1:1151457/1‑100 (MQ=33)                              cGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCt                     <  1:2588153/100‑1 (MQ=33)                              cGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCt                     >  1:647617/1‑100 (MQ=33)                              cGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTACCGCCGGTGCTGGTGCAGATGCTCAACCgg                       >  2:3023844/1‑98 (MQ=12)                               gCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTg                    <  2:1787167/100‑1 (MQ=32)                               gCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTg                    >  2:1826577/1‑100 (MQ=33)                               gCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGCGCTGGTGCAGATGCTCGACCGGCTg                    >  2:2480683/1‑100 (MQ=18)                                ccgcgcCGCAGCCCGGCGGATACCCTTCAGCAGTCCGGCGGCCAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTgg                   >  1:2672255/3‑100 (MQ=255)                                cAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTgg                   >  2:3152049/1‑100 (MQ=33)                                  gcgcCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGaa                 >  2:630893/1‑100 (MQ=32)                                    gccgcAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAg               >  2:3238163/1‑100 (MQ=33)                                    gccgcAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAg               >  2:1831997/1‑100 (MQ=33)                                    gccgcAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAg               <  2:2990229/100‑1 (MQ=32)                                      cgcAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTg             >  1:538352/1‑100 (MQ=32)                                      cgcAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTg             >  2:3423540/1‑100 (MQ=32)                                       gcAGCCTGGCGGATAGCCGTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGa            <  1:3015943/100‑1 (MQ=12)                                         aGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGaaa          >  1:117567/1‑100 (MQ=32)                                         aGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGaaa          <  2:2995738/100‑1 (MQ=33)                                         aGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGaaa          <  2:1870157/100‑1 (MQ=32)                                          gCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAAt         <  1:1850969/100‑1 (MQ=32)                                           ccTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATc        >  2:3124856/1‑100 (MQ=33)                                            cTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATcc       >  2:2409680/1‑100 (MQ=33)                                            cTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATcc       >  1:860902/1‑100 (MQ=33)                                             tGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCt      >  1:3540260/1‑100 (MQ=33)                                             tGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCt      >  1:1328373/1‑100 (MQ=33)                                              gggggATACCCTTCAGCAGTCGGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTTCAGATGCTCGACCGGCTGGAAAGTGAAAt         <  1:127440/93‑1 (MQ=255)                                              ggCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTg     <  1:1356784/100‑1 (MQ=32)                                              ggCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTg     <  1:972044/100‑1 (MQ=32)                                              ggCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTCCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTg     <  1:2479184/100‑1 (MQ=17)                                               gCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTgg    <  1:959826/100‑1 (MQ=32)                                               gCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTgg    <  1:2920872/100‑1 (MQ=33)                                                cGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGc   <  2:822810/100‑1 (MQ=32)                                                cGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGc   <  2:2228321/100‑1 (MQ=33)                                                cGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGc   <  2:1244082/100‑1 (MQ=32)                                                cGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGc   <  1:3409684/100‑1 (MQ=33)                                                cGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGc   >  1:1950299/1‑100 (MQ=33)                                                 ggATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCt  >  2:1131661/1‑100 (MQ=32)                                                 ggATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCt  <  1:1088980/100‑1 (MQ=33)                                                                                                   |                                                  TGAAACCGCCACCGGTGAGCTGGCGAAAACGCAGCGCCGCAGCCTGGCGGATACCCTTCAGCAGTCCGGCGGCGAAGACGGTGGCAGTGTGGTGTTCCCGCCGGTGCTGGTGCAGATGCTCGACCGGCTGGAAAGTGAAATCCTGGCT  >  NC_000913/734630‑734777

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