New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	3741741 =	48 (0.990)	4 (0.090)	4/280	6.9	8.1%	coding (792/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon
	?	NC_000913_3_pae_tpiA	3741759 =	45 (0.960)					coding (774/849 nt)	yiaJ	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GAGAGCGCGTCCCTACTGCTTTGATCCAACGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGC  >  NC_000913_3_pae_tpiA/3741617‑3741905                                                                                                                                               |                                                                                                                                                   gagagCGCGTCCCTACTGCTTTGATCCAACGAAGGAAATGTTAAAGTTTTGGCCCTTGTCCAAAGCGTTATGTGCTCGCGCCCAGGTAATCCCTGACAGTAAATCCCCGTGCATTTGAAATAGCCTCGGCGCTTTCACGCAGTGGTTTc                                                                                                                                              >  2:238743/1‑149 (MQ=255)   gagCGCGGCCCTACTGCCTGAATCCAACGAAGGAAAGGTTAAAGTGTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAg                                                                                                                                            <  1:268097/149‑1 (MQ=255)            ccTACTGCTTTGATCCAACGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGAttttt                                                                                                                                   >  1:488231/1‑149 (MQ=255)              tACTGCTTTGATCCAACGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGACATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGGTTTTtct                                                                                                                                 >  1:778654/1‑149 (MQ=255)                         tCCAACGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGt                                                                                                                      <  1:21357/149‑1 (MQ=255)                            aaCGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGAGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGCAATAGCCTGCGCGGTTTCACGCAGTAGGTTCAGGAGATTTTTCTCTCCCACCTGTTTc                                                                                                                   >  2:440473/1‑149 (MQ=255)                             aCGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCa                                                                                                                  <  1:671489/149‑1 (MQ=255)                               gAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTAGGTGATCGCGGCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGa                                                                                                                <  1:357662/149‑1 (MQ=255)                                aaGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGAc                                                                                                               <  1:813573/149‑1 (MQ=255)                                       tGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGt                                                                                                        <  1:571089/149‑1 (MQ=255)                                                        ttGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGaca                                                                                       <  1:444202/149‑1 (MQ=255)                                                        ttGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGaca                                                                                       >  1:805407/1‑149 (MQ=255)                                                        ttGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGaca                                                                                       >  1:808651/1‑149 (MQ=255)                                                          gTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGGTTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGACATCgccccg                                                                                     >  2:543033/1‑144 (MQ=255)                                                            ccAAAGCGGTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCTAAAGCGAAATCGACACGGc                                                                                   <  2:374886/149‑1 (MQ=255)                                                              aaaGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCTAACGAGAAATGCACACGGCGt                                                                                 >  2:706432/1‑149 (MQ=255)                                                                   gTTATGTGATCGCGCTCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGc                                                                            >  1:137691/1‑149 (MQ=255)                                                                   gTTATGTGATCGCGCTCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGc                                                                            >  1:562806/1‑149 (MQ=255)                                                                            tCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCa                                                                   <  2:618481/149‑1 (MQ=255)                                                                            tCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCa                                                                   >  1:310515/1‑149 (MQ=255)                                                                              gcgcCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATg                                                                 >  1:302003/1‑149 (MQ=255)                                                                                    aGGGCATCCCTGACAGTAAATCCCAGTTCATTAGCGATAGCGTGCGCGGTTTCACTCTGAGCTGTCAGGAGATTTGCGTCTTCTACCTGTTGCAGACTTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCTCCCATGAATATc                                                           <  2:75023/149‑1 (MQ=255)                                                                                       tcctCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCaaa                                                        <  1:729050/146‑1 (MQ=255)                                                                                       gcATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCaaa                                                        <  1:9877/148‑1 (MQ=255)                                                                                         aTCCCTGACAGTAAATCCCAGTTGATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTGTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGGACCCGCCCATGAATATCaaaac                                                      >  2:746071/1‑147 (MQ=255)                                                                                         aTCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAaca                                                      >  2:49195/1‑149 (MQ=255)                                                                                          tCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAacac                                                     >  2:588702/1‑149 (MQ=255)                                                                                            ccTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCg                                                   >  1:378745/1‑149 (MQ=255)                                                                                               gACAGTCAATCCCAGTCTATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCCCCTGTTTCAGACGTGATGTCGAAAGCGAAAGCGACACGGCGTACGGCACCCGCGCATGAATATCAAACACCGGaa                                                <  2:196611/149‑1 (MQ=255)                                                                                                       accccAGTTCATTAGAAATAGCCTGCGCGGGTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATa                                        <  1:171083/147‑1 (MQ=255)                                                                                                         cccAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGCGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACa                                      >  1:32583/1‑149 (MQ=255)                                                                                                            aGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGga                                   <  2:808651/149‑1 (MQ=255)                                                                                                            aGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGga                                   <  2:805407/149‑1 (MQ=255)                                                                                                               tCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGAc                                <  1:451257/149‑1 (MQ=255)                                                                                                                 aTTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACAGGAACAGCAATCCAGGGGCCGc                              >  1:419976/1‑149 (MQ=255)                                                                                                                  ttAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGcc                             >  1:525862/1‑149 (MQ=255)                                                                                                                     gAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAg                          >  1:10671/1‑149 (MQ=255)                                                                                                                      aaaTAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGt                         >  1:322023/1‑149 (MQ=255)                                                                                                                           gCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTAGGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGtt                    <  2:562806/149‑1 (MQ=255)                                                                                                                           gCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGACTTTTCTCCCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGtt                    <  1:501025/149‑1 (MQ=255)                                                                                                                                   ggTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTtctc            <  2:310515/149‑1 (MQ=255)                                                                                                                                   ggTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCCGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTtctc            <  1:369170/149‑1 (MQ=255)                                                                                                                                   ggTTTCACGCAGGGGTTTGAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAAGATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTtctc            <  2:106473/149‑1 (MQ=255)                                                                                                                                      ttCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAAc                                               <  2:495905/111‑1 (MQ=255)                                                                                                                                      ttCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAAc                                               >  1:495905/1‑111 (MQ=255)                                                                                                                                           gcggTGGTTGCAGGAGATTTTTCCCGCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACCCGGCGTACGGCACCCGCCCATGAATATCAAACTCCGGAACAGCAAGACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATc    <  1:714923/146‑1 (MQ=255)                                                                                                                                             aGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATcgc  >  1:82325/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                                   GAGAGCGCGTCCCTACTGCTTTGATCCAACGAAGGAAATGTTAAAGTTTTGGCACTTGTCCAAAGCGTTATGTGATCGCGCCCAGGTCATCCCTGACAGTAAATCCCAGTTCATTAGAAATAGCCTGCGCGGTTTCACGCAGTGGTTTCAGGAGATTTTTCTCTCCCACCTGTTTCAGACGTGATGTCGAAAGCGAAATCGACACGGCGTACGGCACCCGCCCATGAATATCAAACACCGGAACAGCAATACAGGAGACGCCGAGTTCGTTTTCTTCTCTGTCCATCGC  >  NC_000913_3_pae_tpiA/3741617‑3741905

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.