New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	4094416 =	51 (1.610)	5 (0.160)	5/282	3.7	9.9%	noncoding (101/402 nt)	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences	REP299 (repetitive extragenic palindromic) element; contains 9 REP sequences
	?	NC_000913_3_vch_pgi	4094622 =	41 (1.320)					noncoding (307/402 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.

TGTTCTGTGTTCCTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGT  >  NC_000913_3_vch_pgi/4094272‑4094562                                                                                                                                                 |                                                                                                                                                   tGTTCTGTGTTCCTGTAAATCCGGTTTTGTCGGATGCACGAACCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATaa                                                                                                                                                <  1:262850/149‑1 (MQ=255)   ttCTGTGTTCCTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAgg                                                                                                                                              <  1:149730/149‑1 (MQ=255)      tgtgTTCCTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGCTAAGGccc                                                                                                                                           >  2:110881/1‑147 (MQ=255)       gtgtTCCTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACt                                                                                                                                          <  1:70922/149‑1 (MQ=255)           tCCTGTAAATTCGGTGGTGTCGGATCCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTtgtg                                                                                                                                      <  1:212264/149‑1 (MQ=255)            ccTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATCCCGGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGc                                                                                                                                     <  1:492906/149‑1 (MQ=255)             cggTAAAGTCGTGGGTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCAGCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGcc                                                                                                                                    <  2:124004/147‑1 (MQ=17)             cTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGACACTTGTGcc                                                                                                                                    >  2:118971/1‑149 (MQ=255)               gTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGc                                                                                                                                  >  2:470093/1‑149 (MQ=255)                    ttCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATaa                                                                                                                                                <  2:15707/130‑1 (MQ=255)                    ttCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATaa                                                                                                                                                >  1:15707/1‑130 (MQ=255)                    ttCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCg                                                                                                                             >  2:80876/1‑149 (MQ=255)                     tCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCgg                                                                                                                            <  2:25627/149‑1 (MQ=255)                         tgttgtCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATACCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGCTAAGGCCGTGGTGCCGCGTCCGGcaat                                                                                                                        >  1:8995/1‑149 (MQ=17)                         tgttgtCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCAGCCGCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGcaat                                                                                                                        <  1:542470/149‑1 (MQ=255)                            tgtCGGACGCACGCCCCTTAGGCCGGCTAAGGCGGTCGCGCTGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTTCCGACCTGTCGGCCTTATAAGGCACTTGTGCCGCATCCGGcaatcaa                                                                                                                     <  2:179533/149‑1 (MQ=14)                                    gCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGAt                                                                                                             <  1:324297/149‑1 (MQ=255)                                      aCGACCAGTAGGCCGGATAAGGCGCGCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAACGCCTGATGc                                                                                                           <  1:196104/149‑1 (MQ=255)                                             gTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGCCCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGCAGCTg                                                                                                    >  1:80070/1‑149 (MQ=255)                                             gTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCAGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGCTAAGGCACTTGTGGCGCATCCGGCACTCCATTCCTGCCGCCACGcct                                                                                                    >  2:150571/1‑147 (MQ=14)                                                      aTAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCGAATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCtt                                                                                           >  1:81937/1‑149 (MQ=25)                                                          ggCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCa                                                                                       <  1:149616/149‑1 (MQ=40)                                                           gcgcTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCACTGCCTGATGCCACGCTGTCCCCTCTTCTCAg                                                                                      >  2:361795/1‑149 (MQ=11)                                                           gcgcTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGAAATCAATGCCTGGTGCGACGCGCTCGCATcaacactt                                                                                      >  2:361785/1‑142 (MQ=11)                                                                     cgcATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGCCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACt                                                                            <  1:487602/149‑1 (MQ=17)                                                                         tCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGc                                                                                    <  2:363544/137‑1 (MQ=32)                                                                         tCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGc                                                                                    >  1:363544/1‑137 (MQ=33)                                                                                    atGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTg                                                                        <  2:316417/138‑1 (MQ=33)                                                                                    atGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTg                                                                        >  1:316417/1‑138 (MQ=33)                                                                                        cTGATGCTACGCTGTCGCGTTTTATCAGGCCTACAACTATGGCGGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGTAATCGATGCCTGCTGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCTACCTGTAGGCCg                                                         <  2:377922/149‑1 (MQ=11)                                                                                        cTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTcgc                                                                                                >  2:406223/1‑110 (MQ=33)                                                                                             gCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAACGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATaa                                                    <  1:470093/149‑1 (MQ=25)                                                                                               gACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAg                                                                                      >  1:385092/1‑113 (MQ=33)                                                                                                        gcgTCTTATCAGGTCTACACCTATTCCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCTGGATAAGGCACTTGTGc                                         <  2:272742/149‑1 (MQ=255)                                                                                                         cgTCTTATTAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGcc                                        <  1:285908/149‑1 (MQ=37)                                                                                                                  aGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGt                                                                                                   >  1:9870/1‑81 (MQ=35)                                                                                                                  aGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATCAGGCCCTTGTGCCGCATCCGGc                               >  2:504363/1‑149 (MQ=255)                                                                                                                       tACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGcaatca                          >  1:97261/1‑149 (MQ=38)                                                                                                                          aaCTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATg                       >  1:445539/1‑149 (MQ=38)                                                                                                                             tATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTTGGGCGGATAAGGGACTTGTGCCGCATCCGGCAATCGATGCCt                    >  1:152650/1‑149 (MQ=255)                                                                                                                                  ccGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGc                                                                                                      <  1:506659/62‑1 (MQ=37)                                                                                                                                  ccGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGc                                                                                                      >  2:506659/1‑62 (MQ=37)                                                                                                                                  ccGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTg                                                                        <  1:510016/92‑1 (MQ=34)                                                                                                                                  ccGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTg                                                                        >  2:510016/1‑92 (MQ=34)                                                                                                                                  ccGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCGCTTGTGCCGCATCCGGCACTCAATCCCTGATGc               >  2:284447/1‑149 (MQ=255)                                                                                                                                        tGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGca         >  1:138859/1‑148 (MQ=25)                                                                                                                                             gCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTGGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGAGAAGGCACTTGCGCCGCATCCGGCAATAACTGCCTGCTGCGACGCTGTagc    >  2:553981/1‑149 (MQ=11)                                                                                                                                             gCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCgg                                                        >  1:158251/1‑97 (MQ=38)                                                                                                                                             gCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTcgc    <  2:97261/149‑1 (MQ=34)                                                                                                                                               cTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCACTCCCTGCTGCCACTCTGtacctg  >  2:331778/1‑144 (MQ=11)                                                                                                                                               cTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGt  >  2:20105/1‑149 (MQ=33)                                                                                                                                                 |                                                                                                                                                   TGTTCTGTGTTCCTGTAAATTCGGTGTTGTCGGATGCACGACCCGTAGGCCGGATAAGGCGCTCGCGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTATTGCCGACCTGTAGGCCTGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGTCTTATCAGGCCTACAACTGTTGCCGACCTGTAGGCCGGATAAGGCACTTGTGCCGCATCCGGCAATCAATGCCTGATGCGACGCTGTCGCGT  >  NC_000913_3_vch_pgi/4094272‑4094562

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.