New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 1299498	0 (0.000)	37 (0.950)	34/270	0.2	100%	intergenic (+253/‑1684)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
	?	NC_000913_3_pae_tpiA	1300698 =	0 (0.000)					intergenic (+1453/‑484)	ychE/oppA	UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein

TTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  NC_000913_3_pae_tpiA/1299351‑1299646                                                                                                                                                    |                                                                                                                                                     ttctCAAATTACATTTATTTATAAGGATTTCCTTAACTGCTTCTCCTCCCCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAa                                                                                                                                                     <  1:111402‑M1/149‑2 (MQ=255) ttctCAAATTACAGTTAGTTATAAGGCTTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTCCCTTTGGTAACGGAAAGTGCTAAa                                                                                                                                                     >  2:627608‑M1/1‑148 (MQ=255)      aaaTTTCAGTTAGTTATGAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataata                                                                                                                                                <  2:663013‑M1/149‑7 (MQ=255)            cAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaat                                                                                                                                          >  2:281370‑M1/1‑137 (MQ=255)                  gttaTAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGAGTCTTTGTAATCCTGGGCTATCGCAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaa                                                                                                                                    <  1:318030‑M1/149‑19 (MQ=255)                     ataAGGATGTCCTTAACTGCTTCTCCTCACCATCATGTTATTTGCGCCACATCATAATACTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAAGTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaatt                                                                                                                                 <  2:503457‑M1/149‑22 (MQ=255)                                 ttAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttc                                                                                                                     >  2:99866‑M1/1‑116 (MQ=255)                                     gtgCTTCTCCCCACCAATATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAAGGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcacta                                                                                                                 <  1:394103‑M1/148‑38 (MQ=255)                                      tGCTTCTCCCCCCCATCATGATATTTTCGCCACATCATAATCCTTGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactac                                                                                                                <  1:35575‑M1/149‑39 (MQ=255)                                           gtcctcaCCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaa                                                                                                           <  1:168432‑M1/148‑44 (MQ=255)                                                         gTTATATTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAGataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaa                                                                                             <  1:494754‑M1/149‑58 (MQ=255)                                                          ttATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaag                                                                                            >  2:197823‑M1/1‑91 (MQ=255)                                                                           tAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagcca                                                                           >  1:249077‑M1/1‑74 (MQ=255)                                                                             aTCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccact                                                                         <  2:659480‑M1/149‑78 (MQ=255)                                                                                aagggctGGCTGAAGAATAATTGAAATGATATTATGAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctc                                                                      >  2:621513‑M1/3‑69 (MQ=255)                                                                                        gCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgat                                                              <  2:395321‑M1/149‑89 (MQ=255)                                                                                         cTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatct                                                                       >  2:17427‑M1/1‑60 (MQ=255)                                                                                         cTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatct                                                                       <  1:17427‑M1/139‑80 (MQ=255)                                                                                                    ttGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGGTAGataataatcaattgttaaatttttgtgcattttactactggaactgtaatcagaaaagatagacatgattacccaatcactatttgattggattgaaaga                                                  >  2:121826‑M1/1‑49 (MQ=255)                                                                                                     tGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagat                                                 <  2:249077‑M1/149‑102 (MQ=255)                                                                                                         aTGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaactattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgttt                                             <  1:697034‑M1/149‑106 (MQ=255)                                                                                                            atatTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgtt                                          <  1:28839‑M1/149‑109 (MQ=255)                                                                                                              attattAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctct                                                                     <  1:248801‑M1/120‑82 (MQ=255)                                                                                                              attattAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctct                                                                     >  2:248801‑M1/1‑39 (MQ=255)                                                                                                               ttattaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaag                                       <  1:116506‑M1/149‑112 (MQ=255)                                                                                                                tattaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaagg                                      <  1:281370‑M1/149‑113 (MQ=255)                                                                                                                tattaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaagg                                      >  1:252993‑M1/1‑37 (MQ=255)                                                                                                                 attaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                    <  1:632916‑M1/86‑51 (MQ=255)                                                                                                                 attaATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaat                                                                                                    >  2:632916‑M1/1‑36 (MQ=255)                                                                                                                          aCTGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatacttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgca                            >  1:157353‑M1/1‑27 (MQ=255)                                                                                                                            tGCCTTTGGTAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaag                          >  2:559422‑M1/1‑25 (MQ=255)                                                                                                                                     tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaa                           <  2:21710‑M1/139‑124 (MQ=255)                                                                                                                                     tAGAGGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaa                           >  1:21710‑M1/1‑16 (MQ=255)                                                                                                                                      agagGAAATTGCCAAataataatcaatttttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattc                <  1:478786‑M1/149‑135 (MQ=255)                                                                                                                                       gagGAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattct               >  2:363795‑M1/1‑14 (MQ=255)                                                                                                                                          gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgat            >  1:624692‑M1/1‑11 (MQ=255)                                                                                                                                          gAAAGTGCTAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgat            >  1:199853‑M1/1‑11 (MQ=255)                                                                                                                                                  tAAataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcatggatgcaagctatagattctgatacggtcaa    <  1:570394‑M1/149‑147 (MQ=255)                                                                                                                                                    aataataatcaattgttaaattattgtgcatttcactactggaactgtaatcagaaaagatagacatgcttagccaatctctatttgattgaattgaaagatgtttgttaaggcattgatgcaagctatagattctgatacggtcaata  >  1:401785‑M1/1‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                     TTCTCAAATTACAGTTAGTTATAAGGATTTCCTTAACTGCTTCTCCTCACCATCATGTTATTTTCGCCACATCATAATCCTGGGCTTGCTGAAGAATAATTGAAATGATATTATTAATTCCACTGCCTTTGGTAGAGGAAAGTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  NC_000913_3_pae_tpiA/1299351‑1299646

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.