New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	AE015451	2813116 =	38 (0.930)	3 (0.080)	3/300	NT	9.5%	coding (301/1017 nt)	pheS	Phenylalanine‑‑tRNA ligase alpha subunit
	?	AE015451	2813134 =	23 (0.630)					coding (319/1017 nt)	pheS	Phenylalanine‑‑tRNA ligase alpha subunit

TTATCTCGGCAAGAAGGGCGAGCTGACCCAGGTGATGAAGACCCTGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTTCTACTTCAATGCCAACATGCTGCTGCGCACCCACACCTCGCCGGTGCAGGTGCGGACCAT  >  AE015451/2812905‑2813348                                                                                                                                                                                                                                      |                                                                                                                                                                                                                       tccgcacctgcaccggcgaggtgtgggtgcgcagcagcatgttggcattgaagtagaaggtgtcgtgcatcgcccgcgccgggtggtggccagggatgttgagcgcttcgaagttgtggtagtcgtcttccacttctgggccttcggcaatgccgtagccaatgtgggtgaagaactgctcgatgcgctcgagtgtacgggtgatcgggtgCAGGCCACCGGTGGCCTGCAc                                                                                                                                                                                                                      >  2:489529‑M1/212‑232 (MQ=255)   aTCTCGGCAAGAAGGGCGAGCTGACCCAGGTGATGAAGACCCTGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACTCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCAccc                                                                                                                                                                                                                    >  1:305661/1‑232 (MQ=255)                                       aGACCCTGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCAcc                                                                                                                                                                            >  1:680958/1‑236 (MQ=255)                                        gACCCTGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGCCGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCAccc                                                                                                                                                                                                                    <  1:52053/195‑1 (MQ=255)                                             tGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGttctt                                                                                                                                                                                <  1:108134/226‑1 (MQ=255)                                             tGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGttctt                                                                                                                                                                                >  2:108134/1‑226 (MQ=255)                                                      tGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATc                                                                                                                                                                                           <  2:387022/206‑1 (MQ=255)                                                      tGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATc                                                                                                                                                                                           >  1:387023/1‑206 (MQ=255)                                                            ccGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGc                                                                                                                                                        <  1:429770/235‑1 (MQ=255)                                                                    cGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCAccc                                                                                                                                                                           <  2:680957/208‑1 (MQ=255)                                                                      gCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCAccc                                                                                                                                                                                                                    <  2:690852/165‑1 (MQ=255)                                                                            aGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTgg                                                                                                                                       <  1:518703/236‑1 (MQ=255)                                                                                 gcgcgcTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAgac                                                                                                                                  <  1:689394/236‑1 (MQ=255)                                                                                            agggatgttgagcgcttcgaagttgtggtagtcgtcttccacttctgggccttcggcaatgccgtagccaatgtgggtgaagaactgctcgatgcgctcgagtgtacgggtgatcgggtgCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCAcccacct                                                                                                                                                                       <  1:119962‑M1/68‑3 (MQ=255)                                                                                                  gCCAAAGAGCGCGTCCCCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGttc                                                                                                                                                                                  <  2:141184/171‑1 (MQ=255)                                                                                                      aaGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGTCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAg                                                                                                                                                   <  1:254112/198‑1 (MQ=255)                                                                                                                                    acttctgggccttcggcaatgccgtagccaatgtgggtgaagaactgctcgatgcgctcgagtgtacgggtgatcgggtgccggccaccggtggcccgTACCCGGTCACCCGGACACTCGAGCGCGTCGCGCAGGTCTTCACCcaca                                                                                                                                                                        >  2:119962‑M2/99‑147 (MQ=255)                                                                                                                                        ggCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATAGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCgggag                                                                            >  1:737863/1‑233 (MQ=255)                                                                                                                                          cTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAAGGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGc                                                                                                                                                        <  2:35054/157‑1 (MQ=255)                                                                                                                                          atGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATAGACGTCTCCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTCCACCCGCTCACCTGTACACTCGAGCGCATCGAGCAGTTCCTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTa                                                                                                                             <  2:720369/183‑1 (MQ=255)                                                                                                                                           ggccttcggcaatgccgtagcgaatgtgggtgaagaactgctcgatgcgctcgagtgtacgggtgatcgggtgCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCAccc                                                                                                                                                                           >  1:321852‑M1/74‑137 (MQ=255)                                                                                                                                             ccTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCa                                                                       <  1:373745/235‑1 (MQ=255)                                                                                                                                              cTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCAc                                                                      >  1:448344/1‑235 (MQ=255)                                                                                                                                                      aagCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAg                                                                                                               >  2:509553/1‑186 (MQ=255)                                                                                                                                                                  aggtgggtgaagaactgctcgatgcgctcgagtgtacgggtgatcgggtgcaggccaccggtggcctgCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCt                                                                                                 <  1:119962‑M2/120‑1 (MQ=255)                                                                                                                                                                   tgtgggtgaagacctgcgcgacgcgctcgagtgtccgggtgaccgggtaCGGGCCACCGGTGGCCGGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGt                                                                                                                                         >  2:119962‑M1/50‑147 (MQ=255)                                                                                                                                                                      gggtgaagaactgctcgatgcgctcgagtgtacgggtgatcgggtgcaggccaccggtggcctgCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTCGCTACGGCATTGCCGAAGGcc                                                                                                                                                >  1:321852‑M2/65‑137 (MQ=255)                                                                                                                                                                                gCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCg                                                                                                                  >  1:341296/1‑157 (MQ=255)                                                                                                                                                                                         aTTGACGTCGCCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCCCCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAACGCCCAGAAGTGGAAGACGACTACCACAACTTCGaa                                                                                                                <  2:243216/150‑1 (MQ=255)                                                                                                                                                                                               gccACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCgg                                                                               <  2:143735/175‑1 (MQ=255)                                                                                                                                                                                                     cTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCCGTTCTTCACCCACGTTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTGTCACTTCAATGCCAACATGCTGCTGCGCACCca                             >  2:701260/1‑221 (MQ=255)                                                                                                                                                                                                     cTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTTCTACTTCAATGCCAACAtgctg                                        >  2:339613/1‑210 (MQ=255)                                                                                                                                                                                                         cAGGTCGCGGCCAGGCCAACGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTTCTACTTCAATGCCAACATGCTGCTGCGCACCCACACCTCGCCGGTGCAgg            <  1:20465/234‑1 (MQ=255)                                                                                                                                                                                                                 gtgcaggccaccggtggcctgCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTTCTACTTCAATGCCAACATGCTGCTGCGCACCCACACCTCGCCGGTGCAGGTGCGGa      >  2:489529‑M2/22‑232 (MQ=255)                                                                                                                                                                                                                   ccaggccaCCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTTCTACTTCAATGCCAACATGCTGCTGCGCACCCACACCTCGCCGGTGCAGGTGCGGACCAt  <  2:398275/234‑1 (MQ=255)                                                                                                                                                                                                                          accggtggcctgCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACCACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCggg                                                                              >  1:632511‑M2/13‑151 (MQ=255)                                                                                                                                                                                                                                   CTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCa                                                                       >  2:746754‑M1/1‑149 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                       TTATCTCGGCAAGAAGGGCGAGCTGACCCAGGTGATGAAGACCCTGGGCAACCTGCCAGCCGAAGAGCGGCCGAAAGTCGGCGCGCTGATCAACGACGCCAAAGAGCGCGTCACCGTTGTGCTCAATGCCCGCAAGGCTGCCTTTGAAGAAGCCGAGCTCAGCGCTCGCCTGGCTGCCGAATGCATTGACGTCACCCTGCCAGGTCGCGGCCAGGCCACCGGTGGCCTGCACCCGATCACCCGTACACTCGAGCGCATCGAGCAGTTCTTCACCCACATTGGCTACGGCATTGCCGAAGGCCCAGAAGTGGAAGACGACTACCACAACTTCGAAGCGCTCAACATCCCTGGCCACCACCCGGCGCGGGCGATGCACGACACCTTCTACTTCAATGCCAACATGCTGCTGCGCACCCACACCTCGCCGGTGCAGGTGCGGACCAT  >  AE015451/2812905‑2813348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.