New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 1485867	34 (0.630)	5 (0.100)	5/242	NT	12.0%	coding (756/1098 nt)	yhdY	amino acid ABC transporter permease
	?	NC_002947	= 1485897	42 (0.830)					coding (786/1098 nt)	yhdY	amino acid ABC transporter permease

CGCTGATCACCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCTTCATTGCCCTGTTCAAGG  >  NC_002947/1485725‑1486012                                                                                                                                               |                                                                                                                                                  cGCTGATCACCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAg                                                                                                                                             <  5:217497/149‑1 (MQ=255) cGCTGATCACCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAg                                                                                                                                             <  5:222481/149‑1 (MQ=255)      aTCACCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCAt                                                                                                                                        >  5:32912/1‑149 (MQ=255)         aCCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATccc                                                                                                                                     >  3:252428/1‑149 (MQ=255)         aCCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATcc                                                                                                                                      <  8:157693/148‑1 (MQ=255)                tGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGc                                                                                                                              >  5:291216/1‑149 (MQ=255)                 gTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGc                                                                                                                              >  7:27517/1‑148 (MQ=255)                   tCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCa                                                                                                                            <  6:291216/148‑1 (MQ=255)                          gtcgGTTATGCTGCCGTTGTGCATGCCAGAAGGCAGGAGCTTCGACAAGCTGCTGCGGGCGATGATGTGTGTGATCCTGATCCATTCGGGGTACATGGCCGAGGTGGTGCGCGGGGGCCTGCAGGCCATCCGCAAGGGCCAGTACGAAg                                                                                                                    <  2:199866/149‑1 (MQ=255)                             ggTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCttcgtactggcccttggggatggcctgcaggccg                                                                                                                 >  3:65117‑M1/1‑115 (MQ=255)                             ggTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccg                                                                                                                 <  7:255330‑M2/149‑5 (MQ=255)                                 aTGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCttcgtactggcccttggggatggcctgcaggccgccg                                                                                                              <  6:37209‑M1/148‑38 (MQ=255)                                 aTGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgc                                                                                                             <  2:40387‑M2/149‑9 (MQ=255)                                  tgctgcCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCttcgtactggcccttggggatggcctgcaggccgccgc                                                                                                             <  4:65117‑M1/148‑39 (MQ=255)                                  tgctgcCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgcg                                                                                                            >  7:164553‑M2/1‑140 (MQ=255)                                               ccTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCtt                                                                                                <  6:32912/148‑1 (MQ=255)                                                       aaGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTg                                                                                        >  6:245154/1‑148 (MQ=255)                                                       aaGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTg                                                                                        <  5:245154/148‑1 (MQ=255)                                                               aGCTTCGACAAGCGGCTGCGGGCGATGATCGGTGTGATCCTGTTCCCGTGGGCGTACATCGCCGAGGTGGTGGGGGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGAt                                                                               <  2:97149/149‑1 (MQ=255)                                                                     gACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGc                                                                          <  1:40387/148‑1 (MQ=255)                                                                       cAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTgg                                                                       <  6:309379/149‑1 (MQ=255)                                                                            tgctgcGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATc                                                                  >  6:190414/1‑149 (MQ=255)                                                                             gctgcGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCt                                                                 >  1:153404/1‑149 (MQ=255)                                                                                  gggCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCg                                                            <  4:252428/149‑1 (MQ=255)                                                                                      gatgatCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGc                                                           <  1:8142/146‑1 (MQ=255)                                                                                      gatgatCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGc                                                           >  2:8142/1‑146 (MQ=255)                                                                                       atgatCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGgc                                                       <  2:153404/149‑1 (MQ=255)                                                                                              gtgtGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAg                                                >  4:259389/1‑149 (MQ=255)                                                                                                   aTCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTtgt                                           >  3:133138/1‑149 (MQ=255)                                                                                                   aTCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTtg                                            <  4:166081/148‑1 (MQ=255)                                                                                                   aTCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTtg                                            <  6:202727/148‑1 (MQ=255)                                                                                                   aTCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCACAGGCGCTGAAGCTtgt                                           <  5:190414/149‑1 (MQ=255)                                                                                                       tGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCttcgtactggcccttggggatggcctgcaggccgccgcgca                                                                                                          >  5:352997‑M1/1‑41 (MQ=255)                                                                                                       tGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCttcgtactggcccttggggatggcctgcaggccgccgcgca                                                                                                          <  6:352997‑M1/82‑42 (MQ=255)                                                                                                           ccAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGCTCCCCg                                   >  5:184595/1‑149 (MQ=255)                                                                                                             aGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGc                                 <  3:259389/149‑1 (MQ=255)                                                                                                                  gCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGt                            >  3:196288/1‑149 (MQ=255)                                                                                                                      aCATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAac                        >  8:154936/1‑149 (MQ=255)                                                                                                                           gCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCt                    <  7:154936/148‑1 (MQ=255)                                                                                                                            ccGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCtt                   >  4:215488/1‑148 (MQ=255)                                                                                                                             cGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCTTCa                 <  4:196288/149‑1 (MQ=255)                                                                                                                                    gtgCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCTTCATTGccc           <  4:133138/148‑1 (MQ=255)                                                                                                                                     tgCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgcgcaccacctcggcgatgtacgccgactggaaca                                                                            <  6:352997‑M2/82‑42 (MQ=255)                                                                                                                                     tgCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgcgcaccacctcggcgatgtacgccgactggaaca                                                                            >  5:352997‑M2/1‑41 (MQ=255)                                                                                                                                       cgcgGCGGCttcgtactggcccttggggatggcctgcaggccgccgcgcaccacctcggcgatgtacgccgactggaacaggatcacaccgatcatcgcccgcagcagcttgtcgaagctcatgccttctggcaggaacaacggcagca       >  7:164553‑M1/1‑9 (MQ=255)                                                                                                                                        gcggcgGCttcgtactggcccttggggatggcctgcaggccgccgcgcaccacctcggcgatgtacgccgactggaacaggatcacaccgatcatcgcccgcagcagcttgtcgaagctcatgccttctggcaggaacaacggcagcat      <  2:40387‑M1/149‑142 (MQ=255)                                                                                                                                        gcggcgGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgcgcaccacctcggcgatgtacgccgactggaacaggatcacaccgatcatcgcccgcagcagcttgtcgaagctcatgccttctggcaggaacaacggcagca       <  4:65117‑M2/148‑111 (MQ=255)                                                                                                                                         cggcggCCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgcgcaccacctcggcgatgtacgccgactggaacaggatcacaccgatcatcgcccgcagcagcttgtcgaagctcatgccttctggcaggaacaacggcagcat      <  6:37209‑M2/148‑112 (MQ=255)                                                                                                                                           gcggcCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCTTCATTGCCCTGTTCAAg   >  8:148389/1‑149 (MQ=255)                                                                                                                                           gcggcCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCTTCATTGCCCTGTTCAAg   <  8:27517/149‑1 (MQ=255)                                                                                                                                            cggcttcgtactggcccttggggatggcctgcaggccgccgcgcaccacctcggcgatgtacgccgactggaacaggatcacaccgatcatcgcccgcagcagcttgtcgaagctcatgccttctggcaggaacaacggcagcatcacc  <  7:255330‑M1/149‑146 (MQ=255)                                                                                                                                            cggcCTGCAGGCCATCCCCAAGGGCCAGTACGAAgccgccgcgcaccacctcggcgatgtacgccgactggaacaggatcacaccgatcatcgcccgcagcagcttgtcgaagctcatgccttctggcaggaacaacggcagcatcacc  >  3:65117‑M2/1‑34 (MQ=255)                                                                                                                                               |                                                                                                                                                  CGCTGATCACCGTACTGTTCATGTCGTCGGTGATGCTGCCGTTGTTCCTGCCAGAAGGCATGAGCTTCGACAAGCTGCTGCGGGCGATGATCGGTGTGATCCTGTTCCAGTCGGCGTACATCGCCGAGGTGGTGCGCGGCGGCCTGCAGGCCATCCCCAAGGGCCAGTACGAAGCCGCCGCGGCCATGGGCCTTGGCTACTGGCGCTCGATGGGGCTGGTGATCTTGCCGCAGGCGCTGAAGCTTGTGATCCCCGGCATCGTCAACACCTTCATTGCCCTGTTCAAGG  >  NC_002947/1485725‑1486012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ 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.