New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	4094596 =	48 (1.520)	4 (0.130)	4/274	4.1	8.7%	noncoding (281/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913_3_vch_pgi	4094626 =	38 (1.260)					noncoding (311/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

CTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCA  >  NC_000913_3_vch_pgi/4094481‑4094772                                                                                                                                                  |                                                                                                                                                   cTACAACTGTTGCCGACCTGTAGGCCGCATAAGACACTTGTGCCGCATCCGGCAATCAATGCCTGCTGCGACGCTGTCGCGTATTATCAGGCCCACAACTATTACCGACCCTTCGGCCGGATAAGGCACTTGCGCCGCACCCCGcaatc                                                                                                                                                 >  2:248393/1‑149 (MQ=11)      agcatggCCGACCTGGAGGCCGGATAAGGCGCTCGGGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTAGCAGGCCTACAACTCTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGc                                                                                                                                            <  2:384627/143‑1 (MQ=11)      aCTGTTGCCGACCTGGAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTCCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGc                                                                                                                                            <  1:428844/149‑1 (MQ=255)      aCTGTCGCCGACCTGTAGGCCGGAGAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGc                                                                                                                                            <  1:110881/149‑1 (MQ=255)                      aGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTc                                                                                                                            <  1:20105/149‑1 (MQ=34)                                 ggCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCa                                                                                                                 >  1:251586/1‑149 (MQ=32)                                  gCACTTGTTCCGCACCCGGCAATCAAGGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATGGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAg                                                                                                                <  1:104695/149‑1 (MQ=255)                                  gCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCCATGCCTGATGCGACGCTGTCGCGTCTTATCAg                                                                                                                >  1:85167/1‑149 (MQ=17)                                   cACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGAGGGGGTAGGTACTTGTGCCGCATCCGGCAATCAATTCCTGATGCGACGCTGTCGGGGTTTTTCAgg                                                                                                               >  1:268443/1‑149 (MQ=11)                                           ccGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCCCCTCTTATCAGGCCTACCAc                                                                                                       >  2:98886/1‑149 (MQ=12)                                             gCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGACTACAACTATTGCGTGCCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGGGTCTTATCAGGCCTACAACTg                                                                                                     >  2:280500/1‑149 (MQ=11)                                                   ggCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGa                                                                                                                                        >  1:163625/1‑108 (MQ=33)                                                   ggCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGa                                                                                                                                        <  2:163625/108‑1 (MQ=33)                                                   ggCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCg                                                                                               >  1:6028/1‑149 (MQ=32)                                                    gCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTCCAACTGTTGCCGa                                                                                              >  1:110156/1‑149 (MQ=17)                                                    gCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGa                                                                                              >  1:111727/1‑149 (MQ=32)                                                          aatGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTa                                                                                        >  2:407262/1‑149 (MQ=35)                                                             gCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTcgc                                                                                                                          <  1:224549/112‑1 (MQ=32)                                                             gCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTcgc                                                                                                                          >  2:224549/1‑112 (MQ=33)                                                              ccTGATGCGTCGCTGTCGCGTCTTATAAGGCTTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAAAGCCTGATGAGACGCTGTCGCAACTTAAAAGGCCTACAACTGTCGCCGACCCGTAGGcc                                                                                    <  2:548955/149‑1 (MQ=11)                                                               cTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTcgc                                                                                                                          <  1:406223/110‑1 (MQ=32)                                                                     cGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAg                                                                             <  1:410985/149‑1 (MQ=35)                                                                      gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAg                                                                                                                <  2:385092/113‑1 (MQ=32)                                                                         gCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATCAGgcgc                                                                         >  2:549769/1‑149 (MQ=25)                                                                               gcgTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCgcgc                                                                   <  2:251586/149‑1 (MQ=255)                                                                                         aGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGt                                                                                                                             <  2:9870/81‑1 (MQ=33)                                                                                         aGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCGAGCGCCTTATCCGGc                                                         <  1:471305/149‑1 (MQ=11)                                                                                                 aaCTCTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGGGACGCTGTCGCGGCTGAGCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTa                                                 <  2:477436/149‑1 (MQ=17)                                                                                                 aaCTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTCTCAGGCCTACAACTGTTACCGACCCGTAGGCCCGCTAACGCGCTAGCGCCGCATCCGCCAGTGgttc                                                 >  2:478662/1‑148 (MQ=14)                                                                                                    tATTGCCGACCTGTAGACCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTGGCCGACCCGTAGGCCGGCTAAGGCGCNTGCNCCGCATCCGGCAGGGTTTAccc                                              >  1:500456/1‑149 (MQ=14)                                                                                                           ggccTGTAGGCCGGATCAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGa                                       <  1:284447/147‑1 (MQ=255)                                                                                                              cTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGAAGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGCCTc                                    >  2:552540/1‑149 (MQ=255)                                                                                                               tGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCCACTCa                                   >  1:114048/1‑149 (MQ=255)                                                                                                                        gATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGGCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCACAAtttctt                          >  2:463476/1‑149 (MQ=255)                                                                                                                        gATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGCCCGTGTTTACCCGCCGCGACTCAAAAtttctt                          >  1:179306/1‑149 (MQ=255)                                                                                                                         aTAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCTCACCCACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAAtttcttt                         <  1:407262/149‑1 (MQ=255)                                                                                                                                aCTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATaa                  >  1:176763/1‑149 (MQ=255)                                                                                                                                       ccGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCa           <  2:198087/149‑1 (MQ=255)                                                                                                                                           aTCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGCCTCAAAATTTCTTTCTCATAAGGCCGCACGct       >  1:177058/1‑149 (MQ=255)                                                                                                                                                gCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCAGCACGATCTCCa  >  1:313486/1‑149 (MQ=255)                                                                                                                                                gCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTCCCGACCCGTAGGCCGGACAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCa  <  1:511240/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                   CTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAGTGTTTACCCGCGGCGACTCAAAATTTCTTTCTCATAAGCCCGCACGCTCTCCA  >  NC_000913_3_vch_pgi/4094481‑4094772

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.