New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4094664	59 (1.490)	5 (0.200) +ATTGATTGCCGGATGCGGCACAAGTGCCTTATCCGGCCTACAGGTCGGCAATAG	3/174	3.9	12.1%	noncoding (349/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913_3_pae_pgi	= 4284640	NA (NA)					intergenic (‑167/+33)	yjcH/acs	DUF485 family inner membrane protein/acetyl‑CoA synthetase
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGCCATTCGCTACCTGCTGGCGTATCGTGACGTTGGCA  >  NC_000913_3_pae_pgi/4094520‑4094809                                                                                                                                                 |                                                                                                                                                  gtgCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTAc                                                                                                                                               >  1:50269/1‑149 (MQ=32)   gcgccATGCGGTAATCAATGCTTGATGCCACGCGGTCGCGTTTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACaa                                                                                                                                             <  2:211130/145‑1 (MQ=11)    ccGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAAc                                                                                                                                            <  1:203778/149‑1 (MQ=32)            ggCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCg                                                                                                                                    >  1:103618/1‑149 (MQ=32)            ggCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCGGATGCGGCGCTGTCGCGCCTTATCAGGCCTCCGACTGATGCCg                                                                                                                                    >  2:655618/1‑149 (MQ=11)                 tcaatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTAGCGTCTTATCAGGCCTACAACTGTTGCCGACCCg                                                                                                                               >  2:270575/1‑149 (MQ=18)                              ggACGCTGTCGCGTCTGATCAGGCCTACAACTATGGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAg                                                                                                                  <  2:160895/148‑1 (MQ=25)                                aCGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGgc                                                                                                                >  1:463754/1‑149 (MQ=35)                                aCGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCACGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGACAACgc                                                                                                                >  1:86704/1‑149 (MQ=255)                                      tCGGGTCTTATCAGGCGTACAATTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTcgc                                                                                                          <  2:555625/149‑1 (MQ=255)                                      tCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGGGCTcgc                                                                                                          >  1:199048/1‑149 (MQ=38)                                                  aGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCCCGCGCCGCATCCGGc                                                                                              >  2:129442/1‑149 (MQ=255)                                                   ggCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCa                                                                                             >  1:554434/1‑149 (MQ=255)                                                    gCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCACCGCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAg                                                                                            >  1:654629/1‑149 (MQ=255)                                                         cAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTTTTACCAGGCCTACAACTGTGGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGttt                                                                                       <  1:268437/149‑1 (MQ=255)                                                         cAACTATCGCCGACCCGTAGGCCGGATAAGGCACTTGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGttt                                                                                       <  1:268152/149‑1 (MQ=255)                                                            cTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGc                                                                                                                                      <  1:170139/99‑1 (MQ=34)                                                            cTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGc                                                                                                                                      >  2:170139/1‑99 (MQ=34)                                                             tATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAGTCAATGCCTGATGCGCCGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGTCCCGTAGGCCGGATTAGGCGGCCGCGGCGCATCCGGCAGTGTTTAtcc                                                                                   >  1:391877/1‑149 (MQ=17)                                                               ttGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCATGCCTACAACTGTTGCCGACCCGTATGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCcgc                                                                                 >  1:27181/1‑149 (MQ=255)                                                                  ccGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCgcggc                                                                              <  2:571678/149‑1 (MQ=255)                                                                   cGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCgcggcg                                                                             >  2:582345/1‑149 (MQ=255)                                                                    gACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGa                                                                            <  2:653362/149‑1 (MQ=255)                                                                      attgattgCCGGATGCGGCACAAGTGCCTTATCGGGCAATCAATGCCTGATGCGACGCTGTCGCGTGTTGTCAGGCCTACACCTGTTGCCGACCCGTCGGCCGGCTAAGGCGCTCGCGCCCCATCCGGCCGGTCTTCCCCGCGGCGACt                                                                          >  1:526034/8‑149 (MQ=9)                                                                       cTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACACGTAAGCCGCATAAGGCTCGCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTc                                                                         >  1:573244/1‑149 (MQ=17)                                                                        tGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCa                                                                        >  2:547397/1‑149 (MQ=255)                                                                            ggCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAt                                                                    >  1:502619/1‑149 (MQ=255)                                                                             gCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGTGACGCTGTCGCGTATTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtt                                                                   >  1:596695/1‑149 (MQ=255)                                                                             gCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGtt                                                                                                                                        <  1:249067/80‑1 (MQ=34)                                                                             gCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGtt                                                                                                                                        >  2:249067/1‑80 (MQ=34)                                                                             gCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACGCGCGGCGACTCAAAAtt                                                                   >  1:564596/1‑149 (MQ=255)                                                                                ggATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttct                                                                <  1:196568/149‑1 (MQ=255)                                                                                ggATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttct                                                                <  2:554434/149‑1 (MQ=255)                                                                                  aTAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATTCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttcttt                                                              <  1:302355/149‑1 (MQ=255)                                                                                    aaGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATTAGGCCTATAACTGTCGCCGACCCGTACGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATttctttct                                                            <  2:55395/149‑1 (MQ=255)                                                                                      ggCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCATATTTTCATGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCa                                                          <  1:650223/149‑1 (MQ=255)                                                                                       gCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCAt                                                         >  2:590148/1‑149 (MQ=255)                                                                                       cattgattgCCGGATGCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCAt                                                         >  2:689222/8‑149 (MQ=21)                                                                                        cACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAg                                                                                                                  <  2:100736/91‑1 (MQ=34)                                                                                        cACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAg                                                                                                                  >  1:100736/1‑91 (MQ=34)                                                                                                ccGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGGCCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCCAAATTTCGTTCTCATATGCCAGCa                                                >  1:328734/1‑149 (MQ=18)                                                                                                   cATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCa                                                >  2:9964/1‑146 (MQ=255)                                                                                                   cATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCa                                                <  1:9964/146‑1 (MQ=255)                                                                                                        ggCAATCAATGCCCGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACGGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTATTCCTCATTGCCCCGCAAGcacccc                                        <  2:152831/149‑6 (MQ=18)                                                                                                           aatcaatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGc                                     <  1:582345/149‑1 (MQ=255)                                                                                                            atcaatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATaa                                                       >  1:685323/1‑130 (MQ=255)                                                                                                            atcaatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATaa                                                       <  2:685323/130‑1 (MQ=255)                                                                                                             tcaatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCGGCATCCGGCAGTGATTACCGGCGGCGACTCAAAATTTCGTTCTCATCAGCCCGCACGCTCTCCAGCCa                                   >  1:393423/1‑149 (MQ=25)                                                                                                               aatGCCTGATGCGCCGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGCCAtt                                 <  1:437069/149‑1 (MQ=255)                                                                                                               aatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCCGCGACTCAAAACTTCTTTCTCATAACCCCGCCCGCTCTCCACCCAtt                                 >  2:71329/1‑149 (MQ=25)                                                                                                                atGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCg                                                                                                                        <  1:23308/61‑1 (MQ=37)                                                                                                                atGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCg                                                                                                                        >  2:23308/1‑61 (MQ=35)                                                                                                                  gCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAGCTGTTGCCGACCCGGAGGCCGGATAAGACGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAACATTTCTTTCTCATAAGCCCGCACGCTCGCCAGCCATTCGc                              >  1:494878/1‑149 (MQ=37)                                                                                                                          cGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGCCATTCGCTACctgct                      >  1:464443/1‑149 (MQ=255)                                                                                                                                       gcTTATCAGGCCTACAACTGTTCCCGACCCGTCGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGCCATTCGCTACCTGCTGGCGTATCGTGAc         <  1:364408/148‑1 (MQ=255)                                                                                                                                           aTCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttct                                                                >  1:528439/1‑90 (MQ=255)                                                                                                                                           aTCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttct                                                                <  2:528439/90‑1 (MQ=255)                                                                                                                                              aGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGCCATTCGCTACCTGCTGGCGTATCGTGACGTTGGCa  <  1:547397/149‑1 (MQ=255)                                                                                                                                               ggCCTACAACTGTTGCCGACCCGTAGGCCGGATGCGGCGCGAGCGCCTTATCCg                                                                                                >  1:309416/1‑54 (MQ=14)                                                                                                                                                 |                                                                                                                                                  GTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCAGCCATTCGCTACCTGCTGGCGTATCGTGACGTTGGCA  >  NC_000913_3_pae_pgi/4094520‑4094809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.