New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	1978503 =	NA (NA)	29 (1.030)	24/286	0.3	96.7%	intergenic (‑306/+15)	flhD/insB1	flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
	?	NC_000913_3_pae_tpiA	= 2490627	1 (0.040)					coding (1324/1695 nt)	oxc	oxalyl CoA decarboxylase, ThDP‑dependent

TAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1978638‑1978503 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGGAGACGGTGTTGATCTCAGTGGCGC  <  NC_000913_3_pae_tpiA/2490627‑2490488                                                                                                                                                                                                                                                                                      TAATCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGGCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAG                                                                                                                                 <  2:20814/149‑1    CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGGCATTACCGTCGCCATTGAAGGTG                                                                                                                              >  1:46830/1‑149                             CGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAAGCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGAT                                                                                                     <  1:59299/149‑1                                    GACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCATTGGGATGGAAATT                                                                                              >  2:397756/1‑149                                        gacGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAA                                                                                          <  1:214130/146‑1                                         AAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAAC                                                                                         >  2:241621/1‑149                                                        TCAAAATCGGTGGTGCTGCATGTCAAAGTCATCGGGCATTATCTGAACACAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTTAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          <  1:94699/149‑1                                                        TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          >  2:181464/1‑149                                                        TCAAAATCGGTGGAGCTACATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAACAATAAGTTGGAGTCATTACCGTCGCCATTTAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          <  1:190897/149‑1                                                          AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          >  2:273871/1‑147                                                          AAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          <  1:273871/147‑1                                                               CGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCG                                                                   <  1:479662/149‑1                                                                    GAGCCGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGAC                                                              <  1:453690/149‑1                                                                       CTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGAT                                                           >  1:162008/1‑149                                                                         GCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGG                                                                                                                 <  2:8791/93‑1                                                                         GCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGG                                                                                                                 <  2:8727/93‑1                                                                         GCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGG                                                                                                                 >  1:8791/1‑93                                                                         GCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGG                                                                                                                 >  1:8727/1‑93                                                                               CAAAGTCATCGGGCATTATCTGAACAAAAAACACTTTCACTAAGTCGTATTTCTTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAATCGATTTGTCGATATCACCTGCCGGTGACGATCGTTATTT                                                   <  2:104438/149‑1                                                                                 AAGTCATCGGGCATTATCTGAACAGAAAACACTATCAATAAGTTGGAGTCATAAAACTCTGCATCGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTT                                                 <  1:241621/149‑1                                                                                                 TCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCT                                 >  2:435610/1‑149                                                                                                       CATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAG                           <  1:181464/149‑1                                                                                                        ATAAAACACTATCAATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCCGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGG                          >  2:294299/1‑149                                                                                                         TAAAACAGTATCAATAAGTTGGGGTCATTACCGTCGCTATTGAAGGTGATAGTGCTTTTTGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGGA                         <  2:325053/149‑1                                                                                                                     AATAAGTTGGAGTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGGAGACGGGGTTGAT             >  1:371786/1‑149                                                                                                                           TTGGAGTCAGTACCGGCGCCATTGAAGGTGAAAGTGCTATTGGTTTCAGAGGGGTGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGGAGACGGTGTTGGTCTCAGT       >  1:298281/1‑149                                                                                                                                GTCATTACCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGGAGCCGGTGTTGATCTCAGTGGCGC  >  1:250324/1‑149                                                                                                                                       CCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          >  2:136072/1‑70                                                                                                                                       CCGTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAA                                                                          <  1:136072/70‑1                                                                                                                                                                                                                                                                                      TAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_pae_tpiA/1978638‑1978503 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GTCGCCATTGAAGGTGATAGTGCTTTTGGTTTCAGTGGGATGGAAATTGAAACGATTTGTCGATATAACCTGCCGGTGACGATCGTTATTTTTAATAATGGCGGCATCTACAGAGGAGACGGTGTTGATCTCAGTGGCGC  <  NC_000913_3_pae_tpiA/2490627‑2490488

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.