New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 1717760	39 (0.690)	3 (0.060)	3/240	NT	6.8%	coding (459/777 nt)	rsmJ	ribosomal RNA small subunit methyltransferase J
	?	NC_002947	= 1717783	46 (0.880)					coding (482/777 nt)	rsmJ	ribosomal RNA small subunit methyltransferase J

GGCTGGGCAAGGACGCGTTCGTGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGCGCGTGTTCCGGCCTTTGGTGGG  >  NC_002947/1717612‑1717903                                                                                                                                                      |                                                                                                                                                 ggCTGGGCAAGGACGCGTTCGTGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGC                                                                                                                                                  <  2:162400‑M1/149‑1 (MQ=255)   cTGGGCAAGGACGCGTTCGTGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCct                                                                                                                                                <  5:42667/149‑1 (MQ=255)       gCAAGGACGCGTTCGTGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCctgctg                                                                                                                                            <  5:257279/149‑1 (MQ=255)                     gTGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCAt                                                                                                                              >  2:234641/1‑149 (MQ=255)                      tGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATc                                                                                                                             >  7:158310/1‑149 (MQ=255)                             cAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAgcgca                                                                                                                      <  2:85937‑M2/149‑6 (MQ=255)                                ccTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCtcgatggcgttgccggtcagcaggcgcatgc                                                                                                                   <  2:108175‑M1/149‑32 (MQ=255)                                      cTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCt                                                                                                             <  6:185168/149‑1 (MQ=255)                                      cTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCt                                                                                                             <  7:254562/149‑1 (MQ=255)                                      cTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCt                                                                                                             <  4:241866/149‑1 (MQ=255)                                       tGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTg                                                                                                            >  8:119946/1‑149 (MQ=255)                                            gATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAg                                                                                                       <  5:221559/149‑1 (MQ=255)                                              tGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAggg                                                                                                     <  5:164409/149‑1 (MQ=255)                                                  ccTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCtcgatggcgttgccggtcagcaggcgcatgcgc                                                                                                                 <  5:37635‑M1/133‑34 (MQ=255)                                                  ccTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCtcgatggcgttgccggtcagcaggcgcatgcgc                                                                                                                 >  6:37635‑M1/1‑100 (MQ=255)                                                          aGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAg                                                                                         >  8:112728/1‑149 (MQ=255)                                                            cgcCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGt                                                                                       <  1:234641/149‑1 (MQ=255)                                                              ccAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGa                                                                                     <  7:119946/149‑1 (MQ=255)                                                                 gCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGgcgc                                                                                              <  5:370149/137‑1 (MQ=255)                                                                 gCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGgcgc                                                                                              >  6:370149/1‑137 (MQ=255)                                                                 gCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCt                                                                                  <  8:145649/149‑1 (MQ=255)                                                                   cGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTAc                                                                                >  4:147822/1‑149 (MQ=255)                                                                      tGATTGCCGCGCTGCTGGAGGACGGCCTGGCGCGGGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTAc                                                                                >  1:47926/1‑147 (MQ=255)                                                                      tGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTAc                                                                                <  2:47926/146‑1 (MQ=255)                                                                         ttGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGAc                                                                          <  5:175652/149‑1 (MQ=255)                                                                            ccGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGAccc                                                                        >  2:98093/1‑148 (MQ=255)                                                                              gcgcTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGAt                                                                     >  1:25589/1‑149 (MQ=255)                                                                                    ctgGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTc                                                               <  7:112728/148‑1 (MQ=255)                                                                                        aggaCGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCacac                                                          >  5:143700/1‑149 (MQ=255)                                                                                           aCGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACcgc                                                       <  1:85937/149‑1 (MQ=255)                                                                                               ccTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGAc                                                    >  2:73306/1‑148 (MQ=255)                                                                                                cTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACaa                                                  <  1:16665/149‑1 (MQ=255)                                                                                                   gcgc‑gggcgctCGAGGATGAATATGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAaga                                                <  6:251445/148‑1 (MQ=255)                                                                                                             cgAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGt                                      <  6:143700/149‑1 (MQ=255)                                                                                                                   gATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGaaaaa                                <  8:158310/149‑1 (MQ=255)                                                                                                                       aagaagTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTc                                                               >  1:161305/1‑114 (MQ=255)                                                                                                                       aagaagTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTc                                                               <  2:161305/114‑1 (MQ=255)                                                                                                                       aagaagTGGGCCCGATTGTCGGGCGCAGGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGa                             <  5:294817/148‑1 (MQ=255)                                                                                                                          gcatgcgCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATg                         >  2:94059/7‑149 (MQ=255)                                                                                                                             tGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATgcgc                      <  2:25589/149‑1 (MQ=255)                                                                                                                               ggCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGcgcg                     <  3:147822/148‑1 (MQ=255)                                                                                                                                           gggCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGCGCGTGTTc                >  7:311429/1‑141 (MQ=255)                                                                                                                                           gggCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGCGCGTGTTc                <  8:311429/141‑1 (MQ=255)                                                                                                                                            ggCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATGTTTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGCGCGTGTTCCGGCCttt        <  1:98093/149‑1 (MQ=255)                                                                                                                                             gcgcATGCGCCTGCTGACCGGCAACGCCATCGAgcgcatgcgcccgacaatcgggcccacttcttcatccgctcgcgcccgcgccaggccgtcctccagcagcgcggcaatcagcggctggcgctcgatcagg                       <  5:37635‑M2/133‑101 (MQ=255)                                                                                                                                             gcgcATGCGCCTGCTGACCGGCAACGCCATCGAgcgcatgcgcccgacaatcgggcccacttcttcatccgctcgcgcccgcgccaggccgtcctccagcagcgcggcaatcagcggctggcgctcgatcagg                       >  6:37635‑M2/1‑33 (MQ=255)                                                                                                                                              cgcATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGCGCGTGTTCCGGCCTTtggt     <  1:94059/149‑1 (MQ=255)                                                                                                                                               gcATGCGCCTGCTGACCGGCAACGCCATCGAgcgcatgcgcccgacaatcgggcccacttcttcatccgctcgcgcccgcgccaggccgtcctccagcagcgcggcaatcagcggctggcgctcgatcagggtcatctggcagccaagg     <  2:108175‑M2/149‑119 (MQ=255)                                                                                                                                                  tGCGCtcgatggcgttgccggtcagcaggcgcatgcgcccgacaatcgggcccacttcttcatccgctcgcgcccgcgccaggccgtcctccagcagcgcggcaatcagcggctggcgctcgatcagggtcatctggcagccaaggctg  <  2:85937‑M1/149‑145 (MQ=255)                                                                                                                                                      |                                                                                                                                                 GGCTGGGCAAGGACGCGTTCGTGCTGGCCAGCCTTGGCTGCCAGATGACCCTGATCGAGCGCCAGCCGCTGATTGCCGCGCTGCTGGAGGACGGCCTGGCGC‑GGGCGCGAGCGGATGAAGAAGTGGGCCCGATTGTCGGGCGCATGCGCCTGCTGACCGGCAACGCCATCGAGCGCATGCGCGCCTGGGAAGGGGAGGCGCCGCAGGTGATCTACCTCGACCCGATG‑TTTCCACACCGCGACAAGAGCGCCCTGGTGAAAAAGGAAATGCGCGTGTTCCGGCCTTTGGTGGG  >  NC_002947/1717612‑1717903

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.