New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 3584195	NA (NA)	20 (0.380)	18/270	NT	37.7%	intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E
	?	NC_000913_3_pae_pgi	= 3665158	33 (0.620)					coding (653/825 nt)	gadX	acid resistance regulon transcriptional activator; autoactivator

CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/3584063‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACT  <  NC_000913_3_pae_pgi/3665158‑3665016                                                                                                                                                                                                                                                                                      CCTGAATCTGATGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTAAAAATCGTTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTA                                                                                                                                 <  1:326219/149‑1  CTGAATCTGAGGCAGCACTTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTAT                                                                                                                                <  1:22025/149‑1  CTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGGCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGGCATTACCATCACAGCGTGTCGTAT                                                                                                                                >  2:6749/1‑149          GAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTA                                                                                                                        <  2:496541/149‑1                 CACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTCCATATAACCGGGTGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTT                                                                                                                 <  1:779525/149‑1                           GGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGCCAAAGTCATCGGGCATTATCTGAACATAAAACACTATAAATAAGTTGGAGTCATTACCATCAAAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATT                                                                                                       >  1:15091/1‑149                                            CTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACA                                                                                      <  1:974471/149‑1                                              GTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGA                                                                                    <  1:767792/149‑1                                              GTCGTTCTCAAAATCGGGGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGA                                                                                    <  1:459640/149‑1                                               TCGTTCTCAATATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACATCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAG                                                                                   <  2:963561/149‑1                                               TCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTAGAATTTATTATTAGATGACGCCCACAGAG                                                                                   >  1:730657/1‑149                                                     TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCACTAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATacg                                                                             >  1:345566/1‑146                                                     TCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAG                                                                             >  1:342062/1‑149                                                              GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATCAGTTGGAGTCATTACCATCACGGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCG                                                                    <  2:140575/149‑1                                                              GTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTCCGTCTTTCGAAATTATTATGGGATGCCGCCCACAGAACATCACGAACGGTCG                                                                    >  2:250116/1‑149                                                                           ACAAAGTCACCGGGCATGAGCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGT                                                       <  1:130404/149‑1                                                                                   ATCGGGCATTATCTGAACATATAACACTCTTAATAAGTTGGGTTTATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGT                                               <  1:115667/149‑1                                                                                       GGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGCCT                                           >  1:216908/1‑149                                                                                                         AACACTATCAATAAGTTGGAGTCATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTCTTCTGGGATGCCGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTAGAAAAGTGACTCGGCGGCAAGTATTGTTG                         >  1:781916/1‑149                                                                                                                                ATTACCATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACT  >  2:811160/1‑149                                                                                                                                                                                                                                                                                      CCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913_3_pae_pgi/3584063‑3584195 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATCACAGCGTGTCGTATTTCATTTACGTCTTTCGAAATTATTATGGGATGACGCCCACAGAGTATCAGGAGCGATCGGCGCAGAGATTGTCGAACCGTGACTCGGCGGCAAGTATTGTTGCGCAAGGGAATTTTTACGGCACT  <  NC_000913_3_pae_pgi/3665158‑3665016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ 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.