New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	485590 =	21 (1.610)	3 (0.240)	3/238	1.4	13.1%	coding (30/1194 nt)	acrA	multidrug efflux system
	?	NC_000913_3_pae_tpiA	485609 =	20 (1.610)					coding (11/1194 nt)	acrA	multidrug efflux system
Rejected: Frequency below/above cutoff threshold.

TCTGCAGAGGTTCAGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATAC  >  NC_000913_3_pae_tpiA/485466‑485715                                                                                                                             |                                                                                                                              tCTGCAGAGGTTCAGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTTAGCTGCCTGAGTGCATCAGATCGACCGCCAGAGGCGTaaa                                                                                                                    <  1:167367/136‑1 (MQ=255)  cTGCAGAGGTTCAGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACAGCGTGTTATGGCTAAGCTGCCTGAGCGTTTTAGATCGACCGTCAGAGGCGTAAAc                                                                                                                   <  1:126348/136‑1 (MQ=255)              aGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGCACGACCGCCACAGGCGTAAACCCTCTGtttttc                                                                                                       >  2:31407/1‑135 (MQ=255)              aGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTg                                                                                                       >  1:238118/1‑136 (MQ=255)               gTTTTGACTGTTACTACGCCATCGGCTGGCATCTGCGGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGACCGACCGCCAGAGGCGTAAACCCTCCGttttctt                                                                                                      >  2:122137/1‑133 (MQ=255)                        gTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAAAGCATCAGAACGACCGCCAGAGGCGTAAACCATCTGTTTTTGTTCattggta                                                                                             >  2:72112/1‑131 (MQ=255)                           actacGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAAc                                                                                          <  2:128769/136‑1 (MQ=255)                            tagtaagacgataatattaacgcagcaatgggtttattaacttttgaccattgaccaatttgaaatcggacactcgaggtttacatatgaacaaaaaCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAAcc                                                                                         >  2:247290‑M1/98‑136 (MQ=255)                              acGCCAACGACGGGCATCTACTGGCCACCTTGGTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTc                                                                                       >  2:59425/1‑136 (MQ=255)                                             aTCTGCGTGCCACCTTGTTGGCCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCa                                                                        <  2:76922/136‑1 (MQ=255)                                              tCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCaa                                                                       >  1:14048/1‑136 (MQ=255)                                                tgctgGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTcc                                                                               >  1:23848/1‑126 (MQ=255)                                                tgctgGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTcc                                                                               <  2:23848/126‑1 (MQ=255)                                                           ttgttgGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATtggtcaatggt                                                          <  2:219833/136‑1 (MQ=255)                                                            tgttgGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATtggtcaatggtc                                                         >  1:122783/1‑136 (MQ=255)                                                                           tcgtcACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAAcc                                          >  2:112581/1‑136 (MQ=255)                                                                               cacaTCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAAACCAtt                                      >  1:254902/1‑136 (MQ=255)                                                                                                           tttacatatgaacaaaaaCAGAGGCGTAAACCCTCTg                                                                                                             <  2:153215‑M1/19‑1 (MQ=255)                                                                                                           tttacatatgaacaaaaaCAGAGGCGTAAACCCTCTg                                                                                                             >  1:153215‑M1/19‑37 (MQ=255)                                                                                                            agCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTAtattat                      <  2:88186/123‑1 (MQ=255)                                                                                                            agCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTAtattat                      >  1:88186/1‑123 (MQ=255)                                                                                                                   gAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGtacatac  <  2:14048/136‑1 (MQ=255)                                                                                                                     aCGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTaaa                                                                                           <  2:263157/45‑1 (MQ=255)                                                                                                                     aCGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTaaa                                                                                           >  1:263157/1‑45 (MQ=255)                                                                                                                             |                                                                                                                              TCTGCAGAGGTTCAGTTTTGACTGTTACTACGCCAACGGCGGGCATCTGCTGGCCACCTTGTTGGGCCTGTTTGTCGTCACATCCTGTTAGGGCTAAGCTGCCTGAGAGCATCAGAACGACCGCCAGAGGCGTAAACCCTCTGTTTTTGTTCATATGTAAACCTCGAGTGTCCGATTTCAAATTGGTCAATGGTCAAAAGTTAATAAACCCATTGCTGCGTTTATATTATCGTCGTGCTATGGTACATAC  >  NC_000913_3_pae_tpiA/485466‑485715

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.