New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	= 2133461	NA (NA)	4 (0.230)	3/274	2.3	14.3%	noncoding (30/34 nt)	REP145 (repetitive extragenic palindromic) element; contains 1 REP sequences	REP145 (repetitive extragenic palindromic) element; contains 1 REP sequences
	?	NC_000913_3_vch_pgi	3512601 =	24 (1.380)					intergenic (‑257/+33)	yhfZ/trpS	putative DNA‑binding transcriptional regulator/tryptophanyl‑tRNA synthetase
Rejected: Frequency below/above cutoff threshold.

AATGAGGATAAAAAAACCGGGTTTCCCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCAGGAAGGCTTCATC  >  NC_000913_3_vch_pgi/3512454‑3512747                                                                                                                                                    |                                                                                                                                                   aaTGAGGACAAAAAAACCTGGTTTCCCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAt                                                                                                                                                   <  1:133149/149‑1 (MQ=255)                             ggTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGAATCCCGCATGAACAAAGCGCAATTTGCCAGCAATAGt                                                                                                                       <  2:182102/149‑1 (MQ=255)                                ttCAGAGTGCAGATAAAAGCAAAATTGCCTGATGCGCTACGCTTCTCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGaa                                                                                                                    <  2:224574/149‑1 (MQ=255)                                      gTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACgg                                                                                                              <  1:231302/149‑1 (MQ=255)                                       tgatgaTAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTCCATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGc                                                                                                             >  1:109283/1‑149 (MQ=255)                                            atAAAAGCAAAATTCCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGc                                                                                                        <  1:79693/149‑1 (MQ=255)                                                           ccTGATGCGCTACGCTGATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGc                                                                                         >  1:283003/1‑149 (MQ=255)                                                                    gcggattgtttttcataggttgttctcccggcttatgagctggtttgcttgccggataaggcgttcacgccgcatccggcaa                                                                                                                                                   <  2:323967‑M2/2‑2 (MQ=255)                                                                    gcggattgtttttcataggttgttctcccggcttatgagctggtttgcttgccggataaggcgttcacgccgcatccggcaa                                                                                                                                                   >  1:323967‑M2/81‑81 (MQ=255)                                                                          ttATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCttt                                                                          >  1:162456/1‑149 (MQ=255)                                                                            gtCAGGCGTACATTTCCTTGAAATATGTGCATTACTTTGTAGGCCGGATTAGGCGTCCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTa                                                                        <  2:142993/148‑1 (MQ=255)                                                                            aTCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTa                                                                        <  2:219175/149‑1 (MQ=255)                                                                                ggCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCCCGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGAGt                                                                    >  2:58038/1‑149 (MQ=255)                                                                                  ccTACACTTTCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTGCGTACACCGCTTTTAGCTTAc                                                                  <  2:183473/149‑1 (MQ=255)                                                                                   ttACATTTCCTTGCAATATGTGCATTACTTTGGAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCCTTTAGCGTACg                                                                 <  1:198890/148‑1 (MQ=255)                                                                                   cTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACg                                                                 <  2:64578/149‑1 (MQ=255)                                                                                    tACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACgg                                                                >  2:16703/1‑149 (MQ=255)                                                                                            cTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTg                                                        >  2:203902/1‑149 (MQ=255)                                                                                            cTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTg                                                        >  1:120748/1‑149 (MQ=255)                                                                                                          aTTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCttttt                                          >  2:210717/1‑149 (MQ=255)                                                                                                               tttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAACATCCTCTTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCcgcg                                     >  1:223513/1‑149 (MQ=37)                                                                                                                     tgccggatgcggcgtgaacgccttatccggcATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCtt                                                                           <  2:261183‑M2/74‑1 (MQ=255)                                                                                                                     tgccggatgcggcgtgaacgccttatccggcATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCtt                                                                           >  1:261183‑M2/32‑105 (MQ=255)                                                                                                                        cGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCAACAAAACCAATGGCTTGGTACACCGCTTTTAGCGTAGGGGAAGTGGTGGCGTGGGCTTTTTCCGGGGCATCttta                            >  2:16881/1‑148 (MQ=25)                                                                                                                               ggCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCt                     >  1:262094/1‑149 (MQ=255)                                                                                                                                     cccggcgcATCCGGGATGAACAAAGCGCAATTTGCCATCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCa               <  1:96666/144‑1 (MQ=255)                                                                                                                                         ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCAggga           >  2:164909/1‑147 (MQ=255)                                                                                                                                           gcATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCCTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCAGGAAgg         <  1:34283/149‑1 (MQ=255)                                                                                                                                             atccggcATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCAGGAAGGCt       >  1:175500‑M2/8‑149 (MQ=255)                                                                                                                                                  gcATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCAGGAAGGCTTCATc  <  1:263769‑M2/147‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   AATGAGGATAAAAAAACCGGGTTTCCCCGGTTTCAGAGTGATGATAAAAGCAAAATTGCCTGATGCGCTACGCTTATCAGGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCATCACCTGTTGCAGGAAGGCTTCATC  >  NC_000913_3_vch_pgi/3512454‑3512747

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.