New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4525157	45 (0.890)	5 (0.110)	4/240	NT	10.4%	coding (88/1125 nt)	mnmA	tRNA 2‑thiouridine(34) synthase MnmA
	?	NC_002947	= 4525183	44 (0.940)					coding (114/1125 nt)	mnmA	tRNA 2‑thiouridine(34) synthase MnmA

GCGTTTTTCCCCCTTGATACACACCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACTGGGACAAC  >  NC_002947/4525038‑4525330                                                                                                                                                    |                                                                                                                                                    gCGTTTTTCCCCCTTGATACACACCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTCCAGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGga                                                                                                                                                   >  1:53019‑M2/1‑147 (MQ=255)   gTTTTTCCCCCTTGATACACACCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGgaagg                                                                                                                                                <  8:279915‑M2/149‑6 (MQ=255)           cccTTGATACACACCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCa                                                                                                                                        >  3:292675/1‑149 (MQ=255)            ccTTGATACACACCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCAt                                                                                                                                       <  6:91287/149‑1 (MQ=255)                       acCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGACCCCGCGTCAGCGTCGGCATTTCCGGCGGCGTGGAATCTTCCGTCTC‑ACCCATAATGCACAACGAGCAGGGATACCAGGTGGAAGGGATGTTAATgaagacatgg                                                                                                                             >  1:233494/1‑144 (MQ=255)                         cGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTggg                                                                                                                            >  4:49385/1‑147 (MQ=255)                                cATGACCAGACCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGACGGCATGTCAGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGACCAGGGCTAACAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGgac                                                                                                                    >  3:191585/1‑148 (MQ=255)                                  tGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGgacgac                                                                                                                 <  7:279915/149‑1 (MQ=255)                                    aCCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACgg                                                                                                               <  3:61313/149‑1 (MQ=255)                                      cagcccagcACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCa                                                                                                             >  2:182477/1‑149 (MQ=255)                                        gcccagcACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCAcc                                                                                                           >  5:200766/1‑149 (MQ=255)                                        gcccagcACATAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCAcc                                                                                                           <  8:284255/149‑1 (MQ=255)                                           cagcACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGaa                                                                                                        <  4:292675/149‑1 (MQ=255)                                             gcACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATa                                                                                                      <  3:49385/149‑1 (MQ=255)                                                    aaGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCAcc                                                                                               <  6:200766/149‑1 (MQ=255)                                                         cccGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCg                                                                                          >  3:100177/1‑149 (MQ=255)                                                         cccGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCg                                                                                          >  6:4703/1‑149 (MQ=255)                                                           cGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTg                                                                                        <  5:25072/149‑1 (MQ=255)                                                               aaGA‑CCCCCCTCATGGTCGGCATGTCCGGCGCCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTCGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGa                                                                                    <  7:282435/149‑1 (MQ=255)                                                                           cATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACg                                                                         >  2:203505/1‑149 (MQ=255)                                                                               gtcgGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACAGCCCTTGACGACATGGCCTACGACCa                                                                     >  8:297280/1‑149 (MQ=255)                                                                               gtcgGCATGGCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGATCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCa                                                                     <  4:191585/149‑1 (MQ=255)                                                                                  ggCATGTCCGGCTGCGTGGAGTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAgg                                                                   <  7:124321/148‑1 (MQ=255)                                                                                    cATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGaa                                                                                      <  6:213778/127‑1 (MQ=255)                                                                                    cATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGaa                                                                                      >  5:213778/1‑127 (MQ=255)                                                                                    cATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCg                                                                >  4:16338/1‑149 (MQ=255)                                                                                          cggcggCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGAc                                                                                   <  4:82163/124‑1 (MQ=255)                                                                                          cggcggCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGAc                                                                                   >  3:82163/1‑124 (MQ=255)                                                                                          cggcggCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCg                                                          >  6:158972/1‑149 (MQ=255)                                                                                                cgTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTa                                                    >  1:23143/1‑149 (MQ=255)                                                                                                 gTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTAt                                                   <  4:100177/149‑1 (MQ=255)                                                                                                 gTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTAt                                                   <  6:271452/149‑1 (MQ=255)                                                                                                          tCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCg                                                 >  5:79499/1‑142 (MQ=255)                                                                                                          tCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCg                                                 <  6:79499/142‑1 (MQ=255)                                                                                                           ccGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCGAGGCCGTGTGCGACCGTATCGGCATCaa                                          <  1:182477/148‑1 (MQ=255)                                                                                                                tc‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGgaagggctgagacggaagagtccacgccgccggacatgccgacgatgacgcgggtcttggcggggtctttaa                                                                             >  5:87820‑M2/1‑36 (MQ=255)                                                                                                                tc‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGgaagggctgagacggaagagtccacgccgccggacatgccgacgatgacgcgggtcttggcggggtctttaa                                                                             <  6:87820‑M2/108‑73 (MQ=255)                                                                                                                tc‑AGCCCTTCTGCTCATCAAGCAGGGCTACCAGGTGgaagggctgagacggaagagtccacgccgccggacatgccgacgatgacgcgggtcttggcggggtctttaagtgctgggctggtcatgggtaccggtgtgtatcaaggggg                                     <  8:60203‑M2/148‑113 (MQ=255)                                                                                                                    gCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCacac                                 <  2:23143/149‑1 (MQ=255)                                                                                                                     cccTTCTGCTCATCGAGCAGGGCTACCAGGTGgaagggctgagacggaagagtccacgccgccggacatgccgacgatgacgcgggtcttggcggggtctttaagtgctgggctggtcatgggtaccggtgtgtatcaagggggaaa                                  >  7:133139‑M2/1‑32 (MQ=255)                                                                                                                     cccTTCTGCTCATCGAGCAGGGCTACCAGGTGgaagggctgagacggaagagtccacgccgccggacatgccgacgatgacgcgggtcttggcggggtctttaagtgctgggctggtcatgggtaccggtgtgtatcaagggggaaa                                  <  8:133139‑M2/147‑116 (MQ=255)                                                                                                                     cccTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACAcc                                >  6:151022/1‑149 (MQ=255)                                                                                                                        ttCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGAAGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCCTGTGCGACCCTATCGGCATCAAGCTGCACAACGc                              >  3:37575/1‑148 (MQ=255)                                                                                                                                aTCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTc                       <  5:158972/147‑1 (MQ=255)                                                                                                                                aTCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGAGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTcgc                     >  3:171250/1‑149 (MQ=255)                                                                                                                                 tCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTcgcc                    <  5:4703/149‑1 (MQ=255)                                                                                                                                       aGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGaa              >  5:15798/1‑149 (MQ=255)                                                                                                                                         ggCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGc                              <  6:232345/131‑1 (MQ=255)                                                                                                                                         ggCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGc                              >  5:232345/1‑131 (MQ=255)                                                                                                                                           cTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACt          <  5:151022/149‑1 (MQ=255)                                                                                                                                              ccAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACTgg        <  2:233494/148‑1 (MQ=255)                                                                                                                                               cAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACTGGGa      >  4:303081/1‑149 (MQ=255)                                                                                                                                               cAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACTGGGa      >  8:39903/1‑149 (MQ=255)                                                                                                                                                   tGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACTGGGACAAc  <  7:39903/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GCGTTTTTCCCCCTTGATACACACCGGTACCCATGACCAGCCCAGCACTTAAAGACCCCGCCAAGA‑CCCGCGTCATCGTCGGCATGTCCGGCGGCGTGGACTCTTCCGTCTC‑AGCCCTTCTGCTCATCGAGCAGGGCTACCAGGTGGAAGGGCTGTTCATGAAGAACTGGGAAGAGGACGACGGCACCGAATACTGCACCGCCCGTGAAGACCTGGCCGACGCCCAGGCCGTGTGCGACCGTATCGGCATCAAGCTGCACACCGCCAACTTCGCCGCCGAATACTGGGACAAC  >  NC_002947/4525038‑4525330

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ 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.