New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	3423376 =	50 (1.110)	4 (0.090)	4/286	6.5	12.6%	noncoding (3423376/4641682 nt)	repeat_region	repeat region
	?	NC_000913_3_vch_tpiA	= 3946822	6 (0.130)					noncoding (3946822/4641682 nt)	repeat_region	repeat region
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCAC  >  NC_000913_3_vch_tpiA/3423229‑3423522                                                                                                                                                    |                                                                                                                                                    tttCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCCCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGAt                                                                                                                                                    >  2:554755/1‑149 (MQ=255)       aTGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGCCCAACAACAGATAAAAcc                                                                                                                                              >  2:550237/1‑148 (MQ=255)                   tggctttgatGCCTGGCATTTTAGGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTc                                                                                                                                  <  1:206860/145‑1 (MQ=255)                          gatGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGAc                                                                                                                           <  2:584381/149‑1 (MQ=40)                                tGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGcc                                                                                                                     >  2:517680/1‑149 (MQ=38)                                 ggCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGCTAAAACAAAAGGCCCAGTCTTCCGACTGAGCCt                                                                                                                    >  2:299949/1‑149 (MQ=37)                                    aGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACACAAGGCACAGTCTTCCGACTGAGGCtttt                                                                                                                 >  2:407233/1‑149 (MQ=255)                                    aGTTTATGGCGGGCCTCCTGCCCGGCCCCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCtttt                                                                                                                 <  2:422283/149‑1 (MQ=255)                                       tgaTGGGGGGCGTCCTGCACGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTCCCGACTGAGCCTTTTGtt                                                                                                              <  2:93208/147‑1 (MQ=255)                                          tGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTa                                                                                                           >  1:691057/1‑149 (MQ=40)                                             cgggcgCCCGTCCCCGCACCCGCCGGGCCGTTCCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGCGAGCGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTAttt                                                                                                        <  2:29326/149‑1 (MQ=14)                                                 cgTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATg                                                                                                    <  2:267698/149‑1 (MQ=255)                                                     cTGCCCGCCCCCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCATCCACAACCAACGCATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTg                                                                                                <  2:326975/149‑1 (MQ=14)                                                     cTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACCGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTg                                                                                                <  2:718627/149‑1 (MQ=255)                                                                          gTTGCTTGGCAACGTTCAAATCCGGTCCTGGCGGATTTGTCCTACGCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACCCTCGCATg                                                                           <  2:635636/149‑1 (MQ=14)                                                                           ttGCTTCGCAACGTTCAAATCCGCTCTCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATgg                                                                          <  1:716068/149‑1 (MQ=255)                                                                           ttGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATgg                                                                          >  1:516253/1‑149 (MQ=255)                                                                             gCTTCGCAACGTTCAACTCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGCGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACAGCGCCATTTGTGTTATTTGAAGTCTGGCAGTTCCCTACACTCCCacgcgg                                                                        >  2:303818/1‑144 (MQ=11)                                                                                 cGCCACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑Ac                                                                   <  1:289233/149‑1 (MQ=255)                                                                                      cGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGCGCCTTTTGATTTATTTGATGTCTGGCGGTTCCCGACGCTCCAATGGGCAGCAccccc                                                               >  2:13585/1‑148 (MQ=14)                                                                                       gTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCccca                                                             >  2:378900/1‑149 (MQ=255)                                                                                          cacaTCCGCTCCCGGCGGATTGGTCCTACTCGGGAGACTGTTCACCGACAAACACCAGATCACACAAAAGGCCCCGTCTTCCGACTGAGCCTTTTGTTTTATTTGCTGTCTGGCAGTTCCCGACTCTCGCATGGGGAG‑CCCCCACACTa                                                          <  2:442234/146‑1 (MQ=255)                                                                                                cGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATcc                                                    >  1:85612/1‑148 (MQ=255)                                                                                                 tcTCCCAGCGGATTTGTCCTAACTGGTAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTTCTTACTCTCGCATGGGGAG‑ACCCCACACTACCATCgg                                                   <  2:347087/148‑1 (MQ=14)                                                                                                      cggcggATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATggg                                                                         >  1:259447/1‑123 (MQ=255)                                                                                                      cggcggATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATggg                                                                         <  2:259447/123‑1 (MQ=255)                                                                                                          ggATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGc                                          >  2:491812/1‑149 (MQ=255)                                                                                                           gATTTGTCCGACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCAACTCTCGCATGGGGAG‑ACCCGACACGACCAGCAGCGCAAcacgc                                         >  2:626817/1‑145 (MQ=14)                                                                                                             tttGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑Ac                                                                   >  1:101516/1‑121 (MQ=255)                                                                                                             tttGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑Ac                                                                   <  2:101516/121‑1 (MQ=255)                                                                                                                gTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCa                                    >  1:445184/1‑149 (MQ=255)                                                                                                                 tCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTc                                                                                                                               <  1:528606/58‑1 (MQ=255)                                                                                                                 tCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTc                                                                                                                               >  2:528606/1‑58 (MQ=255)                                                                                                                         gggAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCTCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGt                           >  2:672480/1‑149 (MQ=255)                                                                                                                           gagaGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTc                         <  2:533555/149‑1 (MQ=255)                                                                                                                           gagaGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTc                         >  1:679721/1‑149 (MQ=255)                                                                                                                            agagTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCg                        <  2:445184/149‑1 (MQ=255)                                                                                                                                tgtTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGCGTTCGGCAt                    >  1:405039/1‑149 (MQ=255)                                                                                                                                  ttCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCCTgg                  >  2:587839/1‑149 (MQ=255)                                                                                                                                    cACCGACAAACAACAGATAAAACAAGAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGGTCCCTACTCTCCCCTGTGGAA‑AACACACAGGACCATCGGCGCTACCGCGTTTCACTTCTAAGTACGGCATgagg                >  2:715/1‑149 (MQ=11)                                                                                                                                     aCCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGt               <  1:517680/149‑1 (MQ=255)                                                                                                                                       cGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCAc                                   >  1:374575/1‑127 (MQ=255)                                                                                                                                       cGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCAc                                   <  2:374575/127‑1 (MQ=255)                                                                                                                                       cGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCa             >  1:451485/1‑149 (MQ=40)                                                                                                                                          caaacaaCAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGt          <  1:672480/149‑1 (MQ=40)                                                                                                                                           aaacaaCAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTg         <  1:491812/149‑1 (MQ=40)                                                                                                                                               aacaGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGac     <  1:299949/149‑1 (MQ=40)                                                                                                                                               aacaGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGac     >  1:397737/1‑149 (MQ=39)                                                                                                                                               aacaGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGac     >  2:28134/1‑149 (MQ=255)                                                                                                                                                  aGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCGAGTGTTGGATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGaccac  <  1:342386/149‑1 (MQ=14)                                                                                                                                                    |                                                                                                                                                    TTTCGGATGGCCTTTCGCTTGATTTGATGTCTGGCAGTTTATGGCGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAACGTTCAAATCCGCTCCCGGCGGATTTGTCCTACTCGGGAGAGTGTTCACCGACAAACAACAGATAAAACAAAAGGCCCAGTCTTCCGACTGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAG‑ACCCCACACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCAC  >  NC_000913_3_vch_tpiA/3423229‑3423522

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.