New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_002947	= 4841622	49 (0.880)	3 (0.060)	3/242	NT	6.7%	coding (546/609 nt)	ccoO‑II	cbb3‑type cytochrome c oxidase subunit
	?	NC_002947	= 4841652	37 (0.710)					coding (576/609 nt)	ccoO‑II	cbb3‑type cytochrome c oxidase subunit

TCGAGAACAAGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATGGGTGTTCAACCCACGGCGTAAAAAGGACTTCGACG  >  NC_002947/4841504‑4841796                                                                                                                                                     |                                                                                                                                                 tCGAGAACAAGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCaa                                                                                                                                                  <  1:322894/149‑1 (MQ=255)     gaACAAGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggtc                                                                                                                                              <  4:27982‑M2/149‑5 (MQ=255)       aCAAGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggtctt                                                                                                                                            >  8:87558‑M2/1‑143 (MQ=255)        cAAGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggtcttg                                                                                                                                           >  6:154704‑M2/1‑142 (MQ=255)         aaGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggccgcga                                                                                                                                          <  6:44361‑M2/149‑9 (MQ=255)           gCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCa                                                                                                                                        <  7:124425/149‑1 (MQ=255)           gCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAAAGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCa                                                                                                                                        >  3:95728/1‑149 (MQ=255)                   gCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCatcatc                                                                                                                                <  4:313974/149‑1 (MQ=255)                    cAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCatcatc                                                                                                                                >  4:167260/1‑148 (MQ=255)                       ggACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAaga                                                                                                                            <  3:181353/149‑1 (MQ=255)                        gACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAagag                                                                                                                           >  4:202585/1‑149 (MQ=255)                             cgcgAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTgg                                                                                                                                          <  3:13216/129‑1 (MQ=255)                             cgcgAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTgg                                                                                                                                          >  4:13216/1‑129 (MQ=255)                             cgcgAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGc                                                                                                                          >  1:222758/1‑145 (MQ=255)                             cgcgAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGc                                                                                                                          <  2:222758/145‑1 (MQ=255)                             cgcgAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAAc                                                                                                                      <  8:37002/149‑1 (MQ=255)                               cgAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACgg                                                                                                                    <  1:330956/149‑1 (MQ=255)                                    aagaTGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGa                                                                                                                 >  3:351687/1‑147 (MQ=255)                                          gAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGAt                                                                                                          <  7:67827/148‑1 (MQ=255)                                           aaGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATgg                                                                                                        <  3:167260/149‑1 (MQ=255)                                             gTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGat                                                                                                      <  3:27982/149‑1 (MQ=255)                                                    gcACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACca                                                                                                                                     <  3:156059/111‑1 (MQ=255)                                                    gcACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACca                                                                                                                                     >  4:156059/1‑111 (MQ=255)                                                        acTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACcatcat                                                                                                                                 <  4:208812/111‑1 (MQ=255)                                                        acTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACcatcat                                                                                                                                 >  3:208812/1‑111 (MQ=255)                                                            ggCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTcgc                                                                                       <  7:9957/149‑1 (MQ=255)                                                                 cccGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCt                                                                                  >  2:91177/1‑149 (MQ=255)                                                                 cccGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCAACGTCGCGTACCAGGAAGGTCTTGGCACAATCATCAAGCGCACACGGTGACGCTCATGGTTATCGGGATGATGCGCGTCCt                                                                                  >  4:88566/1‑149 (MQ=255)                                                                      acacCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCGAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTgg                                                                                >  7:115056/1‑146 (MQ=255)                                                                      acacCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCGAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTgg                                                                                <  8:115056/146‑1 (MQ=255)                                                                        acCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGAc                                                                                                                <  3:99825/112‑1 (MQ=255)                                                                        acCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGAc                                                                                                                >  4:99825/1‑112 (MQ=255)                                                                        acCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCggg                                                                                                >  4:224427/1‑128 (MQ=255)                                                                        acCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCggg                                                                                                <  3:224427/128‑1 (MQ=255)                                                                          cGACGCCGACTTTGCGGGCGCACGTGACGCGGTAAAGGGCAAGACCGAAATGGACGCCTTCGTCGCGTACCTGCAAGGTCTTGGAACCATCATCACGAGCAAACGGTGACGCTGATGGATATCGGgat                                                                                              <  7:226376/128‑1 (MQ=255)                                                                              gCCGACATTGCCGGCGCACGTGACGCTGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCgtg                                                                     <  3:202585/149‑1 (MQ=255)                                                                                 gACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGTACCGTCgtggtg                                                                  <  3:88115/149‑1 (MQ=255)                                                                                        ccGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCg                                                                                                  <  2:46905/110‑1 (MQ=255)                                                                                        ccGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCg                                                                                                  >  1:46905/1‑110 (MQ=255)                                                                                        ccGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGAtggtgg                                                           >  5:232475/1‑149 (MQ=255)                                                                                                 gTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTgg                                                  <  6:232475/149‑1 (MQ=255)                                                                                                   gACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGc                                                >  7:110515/1‑149 (MQ=255)                                                                                                              gggCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggtcttgcccttgaccgcgtcacgtgcgccggcaatgtcggcgtcggtgtacggggtgccgagtgtgcgcagcacttccatcttcttcgcggtgtccttgccgtcgagc                                     <  5:317946‑M2/149‑110 (MQ=255)                                                                                                               ggCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATgg                                    <  8:110515/149‑1 (MQ=255)                                                                                                               ggCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATgg                                    <  1:91177/149‑1 (MQ=255)                                                                                                                 cAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggtcttgcccttgaccgcgtcacgtgcgccggcaatgtcggcgtcggtgtacggggtgccgagtgtgcgcagcacttccatcttcttcgcggtgtccttgcc                                            <  3:92627‑M2/139‑103 (MQ=255)                                                                                                                 cAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAggtcttgcccttgaccgcgtcacgtgcgccggcaatgtcggcgtcggtgtacggggtgccgagtgtgcgcagcacttccatcttcttcgcggtgtccttgcc                                            >  4:92627‑M2/1‑37 (MQ=255)                                                                                                                 cAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGCTGGCGTTCGTGGGCCTGGCGCTATGGgt                                  <  1:199920/149‑1 (MQ=255)                                                                                                                               aCGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATGGGTGTTCAACCCACGGc                    >  6:352205/1‑149 (MQ=255)                                                                                                                                                 tGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTgg                                                  >  3:68867/1‑101 (MQ=255)                                                                                                                                                 tGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTgg                                                  <  4:68867/101‑1 (MQ=255)                                                                                                                                                  gCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATGGGTGTTCAACCCACGGCGTAAAAAGGACTTcgacg  >  4:320208/1‑148 (MQ=255)                                                                                                                                                   cAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATGGGTGTTCAACCCACGGCGTAAAAAGGACTTcgacg  >  5:53142/1‑147 (MQ=255)                                                                                                                                                     |                                                                                                                                                 TCGAGAACAAGCTCGACGGCAAGGACACCGCGAAGAAGATGGAAGTGCTGCGCACACTCGGCACCCCGTACACCGACGCCGACATTGCCGGCGCACGTGACGCGGTCAAGGGCAAGACCGAAATGGACGCCATCGTCGCGTACCTGCAAGGTCTTGGCACCATCATCAAGAGCAAACGGTGACGCTGATGGATATCGGGATGATTCGCGGCCTGGGCACCGTCGTGGTGATGGTGGCGTTCGTGGGCCTGGCGCTATGGGTGTTCAACCCACGGCGTAAAAAGGACTTCGACG  >  NC_002947/4841504‑4841796

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.