New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	6049480 =	33 (1.280)	3 (0.120)	3/302	NT	9.2%	coding (342/2109 nt)	spoT	bifunctional (p)ppGpp synthase/hydrolase
	?	AE015451	6049563 =	28 (1.140)					coding (425/2109 nt)	spoT	bifunctional (p)ppGpp synthase/hydrolase

GAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAGCGCGCGCGGCAACCGCAAAGAGATCG  >  AE015451/6049330‑6049775                                                                                                                                                                                                                                          |                                                                                                                                                                                                                     gagCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGcaca                                                                                                                                                                                                                    >  1:482721/1‑236 (MQ=255)     cTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACAt                                                                                                                                                                                                                <  1:437841/236‑1 (MQ=255)                          gATGGGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGc                                                                                                                                                                                               <  2:119714/232‑1 (MQ=255)                                  cGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCg                                                                                                                                                                                      >  2:175647/1‑233 (MQ=255)                                             gCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGgc                                                                                                                                                                          <  2:482717/234‑1 (MQ=255)                                                 cGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGTTCGAGGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAg                                                                                                                                                                                 <  1:34562/223‑1 (MQ=255)                                                                 agccagcAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTc                                                                                                                                                      >  1:296541/1‑234 (MQ=255)                                                                           ttGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCg                                                                                                                                                                                      >  1:44476/1‑192 (MQ=255)                                                                                 agaCCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATc                                                                                                                                    <  1:279920/236‑1 (MQ=255)                                                                                    ccGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCAt                                                                                                                                                                      >  2:406963/1‑199 (MQ=255)                                                                                        ggCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAAcc                                                                                                                             <  1:209398/236‑1 (MQ=255)                                                                                          ccGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGc                                                                                                                           <  1:311753/236‑1 (MQ=255)                                                                                                tGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGc                                                                                                                           <  1:408848/230‑1 (MQ=255)                                                                                                     gATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGc                                                                                                                 >  1:439970/1‑235 (MQ=255)                                                                                                        ggggTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAAccc                                                                                                                                                        <  2:194561/193‑1 (MQ=255)                                                                                                                              tGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGAt                                                                                                                   <  2:396759/208‑1 (MQ=255)                                                                                                                                     cGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCt                                                                                <  1:175651/236‑1 (MQ=255)                                                                                                                                                     gcgcAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGAc                                                                                       <  2:240116/213‑1 (MQ=255)                                                                                                                                                        CAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCt                                                                                <  2:173460‑M1/217‑1 (MQ=255)                                                                                                                                                               aaaaCTTCCAGACGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAgg                                                                          <  2:313383/216‑1 (MQ=255)                                                                                                                                                                aaaCTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCtcg                                                      <  1:406967/235‑1 (MQ=255)                                                                                                                                                                    ttCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAAcc                                                                                                                                                         <  2:403732/132‑1 (MQ=255)                                                                                                                                                                             ctggccatggccatggccCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGc                                                                                 <  1:184380/194‑1 (MQ=255)                                                                                                                                                                                   cacgcggatatcgcgggccatggccatggccatcttctggaagttttccgcctgcACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGca                                                                                                                >  2:337520‑M2/56‑158 (MQ=255)                                                                                                                                                                                   cacgcggatatcgcgggccatggccatggccatcttctggaagttttccgcctgcACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGca                                                                                                                <  1:337524‑M2/103‑1 (MQ=255)                                                                                                                                                                                             tcgcgggccatggccatggccatcttctggaagttttccgcctgcACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCgcg                                                 >  2:173304‑M2/46‑210 (MQ=255)                                                                                                                                                                                                  gATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAgcgcgcgc                     >  1:341526/1‑234 (MQ=255)                                                                                                                                                                                                        cgcgTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGaa                                                                                                                                                                                                   <  2:44473/54‑1 (MQ=255)                                                                                                                                                                                                        cgcgTGATCCTGCTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAaga                             <  1:307346/220‑1 (MQ=255)                                                                                                                                                                                                               tCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAGCGCGCGCGGCaa                >  1:456538/1‑226 (MQ=255)                                                                                                                                                                                                                 cTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCCGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTCCGCCCCCATCGCAAACCGCCTGGGTATGCACACCg                                                                                                           >  1:266760/1‑133 (MQ=255)                                                                                                                                                                                                                   ggTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAGCGCGCGCGGCAACCGCAAAGAGAtcg  >  1:189057/1‑236 (MQ=255)                                                                                                                                                                                                                   ggTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCGGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGtt                                                                                              <  2:336245/144‑1 (MQ=255)                                                                                                                                                                                                                                ttccgcctgcACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAGCGCGCGCGGCAACCGc            >  2:286173‑M2/11‑213 (MQ=255)                                                                                                                                                                                                                                    gcctgcACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAGcgcgcgcg                    <  2:296537‑M2/195‑1 (MQ=255)                                                                                                                                                                                                                                          |                                                                                                                                                                                                                     GAGCCTGATGGCGGCCATGCTGCACGATGTGATCGAAGACACCGGCATCGCCAAGGAAGCCCTCAGCCAGCAGTTTGGCGAGACCGTGGCCGAATTGGTCGATGGGGTCAGCAAGCTGACCCAGATGAATTTCGAGACCAAGGCCGAGGCGCAGGCGGAAAACTTCCAGAAGATGGCCATGGCCATGGCCCGCGATATCCGCGTGATCCTGGTCAAGCTGGCCGACCGCCTGCACAACATGCGCACCCTGGAAGTGCTGTCTGGCGAAAAGCGCCGGCGCATTGCCAAGGAAACCCTCGAGATCTACGCCCCCATCGCAAACCGCCTGGGGATGCACACCGTGCGCGTAGAGTTCGAAGACCTTGGCTTCAAGGCCATGCACCCGATGCGCTCGTCGCTGATTCATCGTGCAGTGAAGAGCGCGCGCGGCAACCGCAAAGAGATCG  >  AE015451/6049330‑6049775

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ 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.