New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 694910	48 (1.070)	5 (0.120)	5/282	5.6	9.5%	noncoding (30/98 nt)	RIP61 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site	RIP61 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site
	?	CP009273	2939352 =	50 (1.170)					intergenic (‑151/+88)	tcdA/mltA	tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA/membrane‑bound lytic murein transglycosylase A
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CACCTCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCACCCAGACACGTCCATAG  >  CP009273/2939204‑2939500                                                                                                                                                     |                                                                                                                                                     cACCTCCGAATTAAGAAGGTCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCa                                                                                                                                                      >  2:88644/1‑149 (MQ=255) cACCTCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGTTTTGTAGGCCGGATAAGGCGTCCACGCCGCCTCCGGCa                                                                                                                                                      >  1:358726/1‑149 (MQ=255)  aCCTCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATCTTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAt                                                                                                                                                     >  1:535475/1‑149 (MQ=255)  aCCTCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAt                                                                                                                                                     <  2:136074/149‑1 (MQ=255)   ccTCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATg                                                                                                                                                    <  1:485768/149‑1 (MQ=255)     tCATAATCAAAAAGGGCGAGGTTATCCCGCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTCGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGaa                                                                                                                                                  <  1:1095/149‑1 (MQ=255)     tCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGaa                                                                                                                                                  >  1:291156/1‑149 (MQ=255)         aaTTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGaacaac                                                                                                                                              <  1:284931/149‑1 (MQ=255)           ttAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTCGGCCGGCTAAGCCGTTGACGCGGCATCCGGAATGcacggcgc                                                                                                                                            >  1:167136/1‑144 (MQ=25)             aaaaaGGGCGAGGTTATCCCTCACCCTAAACGCATAAAGGCCTGATGCGCTACGCGTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGAATCGTAGGCCGGATAAGGGGTTCACGCCGCATCCGGCATGAACAACgcgc                                                                                                                                          >  2:472088/1‑149 (MQ=25)             aaaaaGGGCGACATTATCCCTCACCCTAAACGCATAAATGGCTGAGGCGCGACGCTTATCAGGGCTACATGACACCTGCAATATTTTGGATTTGCCTGATTTGTAGGCCGGAAAAGACGTTCACGCCGCATCCGGCATGAACAACgcgc                                                                                                                                          >  2:480285/1‑149 (MQ=21)               aaaGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCAc                                                                                                                                        >  1:509759/1‑149 (MQ=255)                   ggtgagggataaccTCGCCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAg                                                                                                                                    >  1:639089/13‑149 (MQ=21)                    gCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTCCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGt                                                                                                                                   <  1:494558/149‑1 (MQ=255)                     cGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTc                                                                                                                                  <  1:293563/149‑1 (MQ=255)                             tCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCa                                                                                                                          <  2:262100/149‑1 (MQ=255)                                   aCCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACCTAGTCAATAACCAGGAtgt                                                                                                                    >  2:148168/1‑149 (MQ=255)                                     ccTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGATCACGCCGCATCCGGCATGAACAACGCGCACTTAGGCAATAATCAGGATGTGa                                                                                                                  >  2:619699/1‑149 (MQ=255)                                       tAAACGCATACATGCCTGATGCGCTACTCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAgg                                                                                                                <  2:161164/149‑1 (MQ=255)                                       tAAACGCATAAATGCCTGATGCGTCACGATTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAgg                                                                                                                <  1:494003/149‑1 (MQ=255)                                            gCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCCCTTAGTCAATAATCAGGATGTGAGGTTAcc                                                                                                           >  1:716640/1‑149 (MQ=255)                                            gCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTGTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTAcc                                                                                                           <  2:31426/149‑1 (MQ=255)                                             cATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCCCGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTAccc                                                                                                          <  1:506239/149‑1 (MQ=255)                                                  atgccctagtcgcgACGCTTATCAGGCCTACATACCTCCTGCACTCTTTTGGATTTGCATGATTTGTAGGCCGGATACGGCGTTCACGCCGCATCCGGCATGACCAACCCGCACTTAGTCAAGCTTCAGGATGTGAGGTTCCCCCTCAc                                                                                                     <  2:49733/139‑1 (MQ=18)                                                       tGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTCGGCCGGATAGGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTCAGTCAATAATCAGGATATACGGTTGACCCTCACCCTGt                                                                                                >  2:202685/1‑149 (MQ=21)                                                          tGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGGGGTTACCCCTCACCCTGTCat                                                                                             <  2:404851/149‑1 (MQ=255)                                                            cgcTACCGTTTTCGGGCCTACATATCTCCTGCAATATTGTGGATTTGCATGATTTGTAGGCCGGAGAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCatat                                                                                           <  1:62276/149‑1 (MQ=37)                                                                      aTCAGCCCTACCTCACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACTCCTCTCCCTGTCATATCCGTAAAAAc                                                                                 <  2:589290/149‑1 (MQ=37)                                                                           gCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCAt                                                                            >  1:733171/1‑149 (MQ=255)                                                                           gCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCAt                                                                            >  2:55037/1‑149 (MQ=255)                                                                             cTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATAc                                                                          <  1:401743/149‑1 (MQ=255)                                                                                 aTAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGaa                                                                      >  2:510223/1‑149 (MQ=255)                                                                                      tCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCCTCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCGGTCATATCCGTAAAACCCGCATACAGAATATca                                                                 >  1:336544/1‑149 (MQ=255)                                                                                      tCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAGCAACGCGCGCTTAGTCAATAATCAGGATGTGAGGTTACCCCGCACCCTGTCATATCCGTAACAACGGCATACAGAATGTca                                                                 >  2:483042/1‑149 (MQ=37)                                                                                      accTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGCTAATGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTGAATAATCAGGATGTGAGGTTACCCCTGACCCTGTCATATCAGTAAAAACGACATCCAGAatgtaa                                                                 >  2:346848/2‑145 (MQ=37)                                                                                         tGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGGTGTGAGGTTACCCCTCACCCTGTCCTATCCGTAGACGCGGCATACAGAATGTCACAt                                                              >  1:64707/1‑149 (MQ=37)                                                                                           cAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCACCCAGCATATCACATCa                                                            >  1:417859/1‑149 (MQ=255)                                                                                           cAATATTTTGGATTTACATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACAACTGACGCCGTCATGTCCGTAAAAACGGCATACAGAATATCACATCa                                                            >  1:500608/1‑149 (MQ=37)                                                                                                            aTGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTAc                                           >  1:341863/1‑149 (MQ=255)                                                                                                                   gTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGcc                                    >  2:137340/1‑149 (MQ=255)                                                                                                                      ggCTGGATACGGCGCCCGCGCCGCATCCGGCATGCACACCGCGCACTGAGTCAATAAGCAGGATGGGAGGTTGCCCCTCACCCTGTCACATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCgg                                 <  2:1722/149‑1 (MQ=255)                                                                                                                       tccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCCCACTTAGTCAATAATCAGGATGTGATGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCggg                                <  2:424365/148‑1 (MQ=255)                                                                                                                       gCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACCGAATATCCCATCAGCCGCTAAAGACGTTACCCGCGCCCggg                                >  1:300451/1‑149 (MQ=255)                                                                                                                       gCCGGATAACGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCggg                                >  2:292225/1‑149 (MQ=255)                                                                                                                             tAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGtt                          <  1:116315/149‑1 (MQ=255)                                                                                                                             tAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGtt                          <  1:55037/149‑1 (MQ=255)                                                                                                                                    ttCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCa                   <  2:639089/149‑1 (MQ=255)                                                                                                                                          ccgcATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAACCGCCATGCAAAAGGTCACATCAGCCGCTAAAGACGTCACCTGCGCCCGGGGCGGTTTTCAGCACCCAgg             >  1:171688/1‑148 (MQ=255)                                                                                                                                          ccgcATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCGGCTCCCGGGGCGGTTTTCAGCACCCAGa             <  2:341863/149‑1 (MQ=255)                                                                                                                                           cgcATCCGGCATGAACAACGCGCACCTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGCCGTTACCTGCGCCCGTGGGGGTTCTCAGCCCCCCGac            >  1:411620/1‑149 (MQ=255)                                                                                                                                                 cGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCACCCAGACACGTcc      >  2:314667/1‑149 (MQ=255)                                                                                                                                                    cATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTCCCCCTCACCATATCGCATCTTCAAAATCGGAATAATGTAGATCACATCAGCCGCTAATGGCGCGAACACCCCCTGGGCCGGGTTCCGGCACCCAGACACGTCCaga   >  1:174160/1‑147 (MQ=255)                                                                                                                                                    cATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCACCCAGACACGTCCATa   <  1:711380/149‑1 (MQ=255)                                                                                                                                                     aTGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGGCATCTCCGTAAAACCGGCATACAGAATATCACATCAGCCGCTAAAGACGTCACCTGCGCCCGGGGCGCTCTCCAGCCCCCAGACACGGcccaag  >  2:166920/1‑145 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CACCTCAGAATTAAAAAGGGCGAGGTTATCCCTCACCCTAAACGCATAAATGCCTGATGCGCTACGCTTATCAGGCCTACATAACTCCTGCAATATTTTGGATTTGCATGATTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGCGCACTTAGTCAATAATCAGGATGTGAGGTTACCCCTCACCCTGTCATATCCGTAAAAACGGCATACAGAATATCACATCAGCCGCTAAAGACGTTACCTGCGCCCGGGGCGGTTTTCAGCACCCAGACACGTCCATAG  >  CP009273/2939204‑2939500

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ 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.