New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1979271 =	0 (0.000)	26 (0.670)	25/474	0.6	100%	intergenic (‑56/‑482)	insA5/uspC	IS1 family protein InsA/universal stress protein C
	?	NC_000913	= 2102947	NA (NA)					pseudogene (443/446 nt)	wbbL	interrupted rhamnosyltransferase WbbL

CCAGCGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTCATGATGATATCGGGATTCAAAAACAAAATGTAATCATCATCTGCGGGTCTATATTTTTCCTTTACATACGCCACCGCAATATTAT  >  NC_000913/2102704‑2103193                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                       ccAGCGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTa                                                                                                                                                                                                                                                  >  2:185437/1‑250 (MQ=32)       gATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATaaa                                                                                                                                                                                                                                           <  1:321033/251‑1 (MQ=34)             gTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGacac                                                                                                                                                                                                                                     <  1:185437/251‑1 (MQ=38)                  cGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATaa                                                                                                                                                                                                                                <  2:226424/251‑1 (MQ=40)                          aCCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAACTCAGa                                                                                                                                                                                                                         >  2:245224/1‑250 (MQ=255)                              gCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGc                                                                                                                                                                                                                     >  1:204726/1‑250 (MQ=255)                                  tGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACAGAAATGACACAATAAAATCAGAAAGcaca                                                                                                                                                                                                                  <  2:401988/249‑1 (MQ=255)                                                 cGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACg                                                                                                                                                                                                   <  1:2116/249‑1 (MQ=255)                                                    tGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGaat                                                                                                                                                                                               >  2:357097/1‑250 (MQ=255)                                                                     tGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTc                                                                                                                                                                              <  1:245224/250‑1 (MQ=255)                                                                                   cTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAAc                                                                                                                                                               >  1:143617/1‑251 (MQ=255)                                                                                          aTGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCAt                                                                                                                                                         >  2:194187/1‑250 (MQ=255)                                                                                          aTGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATa                                                                                                                                                        <  2:188406/251‑1 (MQ=255)                                                                                               ggACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGt                                                                                                                                                    >  2:173319/1‑250 (MQ=255)                                                                                                 aaaaGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGAATTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACt                                                                                                                                                 <  2:17094/249‑1 (MQ=255)                                                                                                      aaaaTCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTa                                                                                                                                                >  1:38835/1‑247 (MQ=255)                                                                                                      aaaaTCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTa                                                                                                                                                <  2:38835/247‑1 (MQ=255)                                                                                                        aaTCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGc                                                                                                                                           >  1:353408/1‑250 (MQ=255)                                                                                                           ctctTTTCTGGTATGACGGCGCTTACTGCTGACTTCCCTGTCGGCGAAGGTAACTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAACCATGATCTCATATCAGGGACTTGTTCGCACCTTACTTAATCCCTACCATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTACAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATa                                                                                                                                        >  2:184045/1‑250 (MQ=25)                                                                                                            tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACa                                                                                                                                                              >  1:108964/1‑227 (MQ=255)                                                                                                            tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACa                                                                                                                                                              <  2:108964/227‑1 (MQ=255)                                                                                                             ctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCAt                                                                                                                                         <  2:354556/247‑1 (MQ=255)                                                                                                                 tCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCGTCAGCTCGGAACAGGCATAATGTACTAAAAGCATAACGCtt                                                                                                                                  <  1:184045/250‑1 (MQ=255)                                                                                                                            ggCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACat                                                                                                                       >  2:335923/1‑250 (MQ=255)                                                                                                                              cgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGGACTAAAAGCATAACGCTTACTTTCGACATAtt                                                                                                                    <  2:16379/251‑1 (MQ=255)                                                                                                                                        tgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAat                                                                                                                <  2:386339/245‑1 (MQ=255)                                                                                                                                        tgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAat                                                                                                                >  1:386339/1‑245 (MQ=255)                                                                                                                                                           ggTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTc                                                                                       <  1:194187/251‑1 (MQ=255)                                                                                                                                                                  tgatgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTCatgaag                                                                                 <  2:30363/250‑3 (MQ=255)                                                                                                                                                                                                                                             ttccttAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTCATGATGATATCGGGATTCAAAAACAAAATGTAatc                                                    <  2:21165/204‑1 (MQ=255)                                                                                                                                                                                                                                             ttccttAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTCATGATGATATCGGGATTCAAAAACAAAATGTAatc                                                    >  1:21165/1‑204 (MQ=255)                                                                                                                                                                                                                                                  tAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTCATGATGATATCGGGATTCAAAAACAAAATGTAATCATCATCTGCGGGTCTATATTTTTCCTTTACATACGCCACCGCAAtattat  <  2:353408/249‑1 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                       CCAGCGGATAAGGTCGCCGGCCATTACCAGCCTTGGGGTAAAACGGCTCGATGACTTCCACCATGTTTTGCCATGGCAGAATCTGCTCCATGCGGGACAAGAAAATCTCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAATCCCTAACATAAATGACACAATAAAATCAGAAAGCACAGGAAATTTTCTTACGGAATAATCATGTAAAGATTTCGCTTCATCTCGGAACAGGCATAATGTACTAAAAGCATAACGCTTACTTTCGACATATTTAATATATGTCAGCAAATCATCATGCTTCATGATGATATCGGGATTCAAAAACAAAATGTAATCATCATCTGCGGGTCTATATTTTTCCTTTACATACGCCACCGCAATATTAT  >  NC_000913/2102704‑2103193

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ 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.