New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	3583428 =	NA (NA)	25 (0.470)	25/270	NT	43.1%	intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
	?	NC_000913_3_pae_pgi	3665150 =	33 (0.620)					coding (661/825 nt)	gadX	acid resistance regulon transcriptional activator; autoactivator

GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3583561‑3583428 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTA  >  NC_000913_3_pae_pgi/3665150‑3665287                                                                                                                                                                                                                                                                                  ggCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCACCACCCGCTGTGATATCCAC                                                                                                                             <  1:674373/147‑1                                  CGTCAGTAGCTAAACAGGCGGGACAGCTGATATAACGTGAAGCCCCTGTAGCACCTCAAAACTACCATCATACCCTAGATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCAT                                                                                            <  2:305116/149‑1                                   GTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATG                                                                                           <  1:537113/149‑1                                        TAGCTGAACAGGAGGGACAGCTGATAGAAACAGATGCTATTGTAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAA                                                                                      <  1:385550/149‑1                                              AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAA                                                                                >  1:750909/1‑149                                                  GGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACCCGCTTAATTGAAAAACCATGTATAACAATAAGTTG                                                                            <  1:44231/149‑1                                                                        GAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTCCAAAGCACGTTACATTCTACAC                                                      >  2:597902/1‑149                                                                         AAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACT                                                     >  2:64723/1‑149                                                                           GCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCA                                                   <  1:516349/149‑1                                                                               CTGGAGCACCTCAAAATCACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCACAGCACGTTGCATTCTACACTCAGTAA                                               <  2:902922/149‑1                                                                                   AGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGAAAAGCACGTTGCATTCTACACTCAGTAAGAAA                                           >  2:648539/1‑149                                                                                         TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGA                                     >  1:486001/1‑149                                                                                           AAAACCACCATCATACACTAAATCAGGAAGTTGGCAGCATCACCCGTTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAAT                                   <  1:413456/149‑1                                                                                           AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACT                                                                                                                     >  2:310862/1‑67                                                                                           AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACT                                                                                                                     <  1:310862/67‑1                                                                                                CACCCTCATATACTAAATCAGAAAGTTGGCACCATCACCGGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGAT                              <  2:328437/149‑1                                                                                                 ACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAGGCAACTGTGAATATTATG                             >  2:206694/1‑149                                                                                                     TCATACACTAAATCAGTAAGTTGGCAGGATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTC                         <  2:39488/149‑1                                                                                                     TCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTC                         >  1:592806/1‑149                                                                                                        tcCACTAAATCAGGAAGTACGCAGCATCACCCGCTGGGAGATCCCCAGGATACTGCAACTCGCTTAATTGAAAATCCATGTATAACAAGAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTC                      <  1:480355/147‑1                                                                                                        TACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTC                      >  1:14248/1‑149                                                                                                               AATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTAAGTAAGGAACTGTGGTTATGATGTCTCTTATTCGCGC               >  2:843002/1‑149                                                                                                                      AAGTTGGCAGCATCACCCGGTGTGAGATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTGTCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTT        <  2:309333/149‑1                                                                                                                          tgggatCATCACCCGCTGTGATATCCACAGGATACTGCATCTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCACATCACGTTGCATTCTACACTCAGTAAGCAACTGTGTATATGATGTCTCTTCTTCGCGCAATTTTTTCTT    <  2:824865/143‑1                                                                                                                            GCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACACTAATTTGCAAAGCACGTTCGTTGGTACACTCAGTAAGCAACTATGAATATGATGTCTCTTCTTCACGCAATTTTTTCTTTA  >  1:736050/1‑149                                                                                                                                                                                                                                                                                  GTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_pgi/3583561‑3583428 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTA  >  NC_000913_3_pae_pgi/3665150‑3665287

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.