New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	2689525 =	36 (0.880)	3 (0.080)	3/316	NT	9.0%	coding (955/2268 nt)	PP_2356	putative Phytochrome family protein
	?	AE015451	2689657 =	27 (0.700)					coding (823/2268 nt)	PP_2356	putative Phytochrome family protein

TGGTCGGCCATGGACGAGATCATGCGTACGATGTGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGTTGACCCGGTACAGCTCGCGCGCCTGGCGCGGGATGTCTGCAGCCGG  >  AE015451/2689425‑2689849                                                                                                                                                                                                                                         |                                                                                                                                                                                                 tGGTCGGCCATGGACGAGATCATGCGTACGATGCGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCa                                                                                                                                                                                                >  1:338998/1‑235 (MQ=255)      ggCCATGGACGAGATCATGCGTACGATGTGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGt                                                                                                                                                                                             >  2:495365/1‑233 (MQ=255)      ggCCATGGACGAGATCATGCGTACGATGTGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTg                                                                                                                                                                                           <  1:383508/235‑1 (MQ=255)                     cATGCGTACGATGTGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGt                                                                                                                                                                           >  1:340003/1‑236 (MQ=255)                          gTACGATGTGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACg                                                                                                                                                                      >  1:648549/1‑236 (MQ=255)                            aCGATGCGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTg                                                                                                                                                                          <  2:338997/230‑1 (MQ=255)                                tgtgCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGAt                                                                                                                                                                >  1:762916/1‑236 (MQ=255)                                     tGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGAtacgct                                                                                                                                                           >  1:755969/1‑236 (MQ=255)                                       gcgcAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGAtacgct                                                                                                                                                           <  2:762915/234‑1 (MQ=255)                                               tCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTAcgcagcg                                                                                                                                                   >  1:746796/1‑234 (MQ=255)                                                 aaCAGCGTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTAcgcagcgcag                                                                                                                                                <  1:236422/235‑1 (MQ=255)                                                                              gcgGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAgg                                                                                                                                                                            >  2:255723/1‑178 (MQ=255)                                                                                gggACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTgcgc                                                                                                                >  1:423980/1‑236 (MQ=255)                                                                                               gCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAACCTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGCCGCggg                                                                                                  >  2:248627/1‑235 (MQ=255)                                                                                                     GCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCCCGGGCGAtacgct                                                                                                                                                           <  2:659769‑M1/172‑1 (MQ=255)                                                                                                           tggcttcgatgtcgctgtcgatcgtgcttgacggccagctgtgggggctgatttcctgccaccatcaacagccacgcccggtggacctgcgcacccgcacggcctgcgagctgttggccagcgtgcCCATGTTGCGCATGTACTGCAGGTg                                                                                                                                                                          <  1:441101‑M2/25‑1 (MQ=255)                                                                                                                      tCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGt                                                                           >  1:451926/1‑235 (MQ=255)                                                                                                                          aGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCg                                                                                                                      >  2:512502/1‑188 (MQ=255)                                                                                                                          aGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCa                                                                      >  1:535689/1‑236 (MQ=255)                                                                                                                               gTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTc                                                                 <  1:495366/236‑1 (MQ=255)                                                                                                                                tGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTc                                                                 <  1:597120/235‑1 (MQ=255)                                                                                                                                                cACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTg                                                                                <  2:755968/204‑1 (MQ=255)                                                                                                                                                              tttcctgccaccatcaacagccacgcccggtggacctgcgcacccgcacggcctgcgagctgttggccagcgtgcCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTgg                                                                        >  2:259142‑M2/76‑198 (MQ=255)                                                                                                                                                                       ggCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCt                                                                                                                           <  1:491255/138‑1 (MQ=255)                                                                                                                                                                       ggCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCt                                                                                                                           >  2:491254/1‑138 (MQ=255)                                                                                                                                                                       ggCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATAc                                                   >  1:610254/1‑210 (MQ=255)                                                                                                                                                                       ggCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATAc                                                   <  2:610253/210‑1 (MQ=255)                                                                                                                                                                          atcaacagccacgcccggtggacctgcgcacccgcacggcctgcgagctgttggccagcgtgcCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGTTGACCCGGTACa                                    >  1:570508‑M2/64‑222 (MQ=255)                                                                                                                                                                                             cTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCAATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATAc                                                   <  1:754709/188‑1 (MQ=255)                                                                                                                                                                                                      aaCCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGtt                                               <  2:417248/183‑1 (MQ=255)                                                                                                                                                                                                        ccACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGTTGCCCCGGTACAGCTCGCGCGCCTGGCGCGGGATGTCTGCAGCCgg  >  1:602955/1‑226 (MQ=255)                                                                                                                                                                                                                  cAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTg                                                                                                          <  2:366414/112‑1 (MQ=255)                                                                                                                                                                                                                            gAAGCCAGCGTGCCCATGTTGCGCATGGACGGCAGGTGCACGGGCGATGCGCTACGCAGCGCAGCAAAACTCAGGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTg                                                                                          <  2:131745/118‑1 (MQ=255)                                                                                                                                                                                                                                  agcgtgcCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCCGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGTTGACCCGGTACAGCTcgcg                             >  2:47717‑M2/8‑173 (MQ=255)                                                                                                                                                                                                                                     gtgcCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTgc                                                                                                                  >  2:508039‑M2/5‑85 (MQ=255)                                                                                                                                                                                                                                     gtgcCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGGTGACCCGGTACAGCTCGCGCGCCt                        >  2:144679‑M2/5‑175 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                 TGGTCGGCCATGGACGAGATCATGCGTACGATGTGCTGGCGCAGCGTCAACAGCTTGCGCGTACTGGCATGGGACTCGCGGGACTCTATCTGCAGCGACAGCACGCTGGCCAACAGCTCGCAGGCCGTGCGGGTGCGCAGGTCCACCGGGCGTGGCTGTTGATGGTGGCAGGAAATCAGCCCCCACAGCTGGCCGTCAACCACGATCGACAGCGACATCGAAGCCAGCGTGCCCATGTTGCGCATGTACTGCAGGTGCACGGGCGATACGCTACGCAGCGCAGCAAAACTCATGTCCAGCGGCTTGCCGGTGCGCGGGTTGGTAGCGGGCAGCAGTGGCGAGGGCTGATAGTTGGCATCTTCGATCACGCGGATACGGTTGACCCGGTACAGCTCGCGCGCCTGGCGCGGGATGTCTGCAGCCGG  >  AE015451/2689425‑2689849

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.