New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	50 (0.920)	41/296	0.3	100%	intergenic (+146/‑127)	insH1/ynaJ	IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
	?	CP009273	= 1972751	0 (0.000)					intergenic (‑297/‑483)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

TAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAG  >  CP009273/1391360‑1391642                                                                                                                                        |                                                                                                                                                    tAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAAt                                                                                                                                        <  2:498083/149‑1 (MQ=35)       cTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGttt                                                                                                                                  >  1:31322/1‑148 (MQ=40)       cTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTg                                                                                                                                  >  2:74525/1‑149 (MQ=40)        ttcaaTGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGa                                                                                                                                 <  2:7250/146‑1 (MQ=255)         tAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAt                                                                                                                                <  2:457329/149‑1 (MQ=255)                cGAAGAAACGGTCGAAATAGACTAATTCAAGGCATTGACGAGAGAACACACCGACGCAAACAGAAAGAAATGAAAAGACTGAGTCAGACGAGAAGAATTTCCCCGCTTATTCGCACCATCCCTAACTAATCAATCCCTGGAATGTaaag                                                                                                                         >  1:467361/1‑148 (MQ=2)                 gaagaaACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCGCCGCGTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTaatac                                                                                                                        >  1:809217/1‑146 (MQ=255)                       aCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGGCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTa                                                                                                                  >  2:380102/1‑149 (MQ=255)                       aCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTa                                                                                                                  >  2:459176/1‑149 (MQ=255)                                     cTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGtttt                                                                                                    >  2:262611/1‑149 (MQ=255)                                     cTGACTCTAGGCATTTGCGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAACTGACTGGTTCAGCCGAGAAGAATTGCCCCCCTTATTCGGACCTTCCCTAACTAATCAATGCGGTGATTGTAAATCCAGCTAAGAGGTCAGGtttt                                                                                                    <  1:700576/149‑1 (MQ=18)                                       gATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCa                                                                                                  <  1:390820/149‑1 (MQ=255)                                           cAAGGAATTGACGGGAGAAAACATCGGCGCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCGAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGc                                                                                              <  1:52152/149‑1 (MQ=21)                                                 aTTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGGAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTTAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACaa                                                                                        >  2:641559/1‑149 (MQ=255)                                                       gggAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTCCTCCCGTCGCGCGTTGTAAATCCAGCGAAGAGGTGAGGGTTTCCGAGCCGACAACGGTGa                                                                                  >  2:427709/1‑149 (MQ=14)                                                        ggAGAAAAAATCGGCTCGAACATGAAGAAATGAAATGACTGAGTCAGCCGACAAGAATTACCCCGCTTATTAGCACCTTCCCTTAATAATCAATGCGTTGATTATAACTCGAGCTCAGAAGAGGGGGTTTCAGAGCGGACAAAGGAGaa                                                                                 >  1:358176/1‑149 (MQ=17)                                                                        cAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCAGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGtt                                                                 >  2:615224/1‑149 (MQ=255)                                                                         aaaCATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCTTTGATTGTAAATCCAGCTAACAGGTGAGGTTTTCAGAGCAAACAACGGTGAAATGTCATGGTATTGTTa                                                                >  1:7378/1‑149 (MQ=255)                                                                           aCATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACg                                                              >  2:95785/1‑149 (MQ=255)                                                                                aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                                         <  1:649032/149‑1 (MQ=255)                                                                                aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAAGCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                                         <  2:35235/149‑1 (MQ=255)                                                                                aagaaATGAAATGACTGAGTCAGCAGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                                         <  1:736076/149‑1 (MQ=255)                                                                                aagaaATGAAATGACTGAGCCAGCCTAGAAGACTTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                                         <  2:809217/149‑1 (MQ=255)                                                                                    aatgcaccgaCTGAGTCAGCCGAGAAGTATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGCATTGTTACGTTTAGGTaa                                                     <  2:867728/141‑1 (MQ=38)                                                                                      tgaaatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACa                                                   <  1:401399/149‑1 (MQ=255)                                                                                             aCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATCGTATTGTTACGTTTAGGTAACAAGAAAtt                                            <  2:566178/149‑1 (MQ=255)                                                                                              cTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAAGGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAAttt                                           <  2:427276/149‑1 (MQ=255)                                                                                                     aGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGca                                    >  2:160734/1‑149 (MQ=255)                                                                                                       ccGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGcaca                                  >  1:768612/1‑149 (MQ=255)                                                                                                                     cccGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGACGTTCGGGGTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAGCAAGAAATTTGTCTGCCCACGGATTACACCATg                    >  2:349963/1‑149 (MQ=255)                                                                                                                       cGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAAGATTAcctcatcct                  >  1:663865/1‑146 (MQ=255)                                                                                                                             ttCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCATAAGGATTACATCATGATTATGGc            <  2:469525/149‑1 (MQ=255)                                                                                                                                 ccccTTCCCTAACTGAGCTATGCGTTGACTGTAAATCCAGCTGAGACGTGAGGTTTTCCGCGCCGACAACGGTGCAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTCAACAAGGATTACATCATGATTATGGCGaaa        <  1:90657/147‑1 (MQ=255)                                                                                                                                    cTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTg     >  1:351508/1‑149 (MQ=255)                                                                                                                                      tCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGaa   <  1:74525/149‑1 (MQ=255)                                                                                                                                       cccTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAg  >  1:157971/1‑149 (MQ=255)                                                                                                                                        |                                                                                                                                                    TAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAG  >  CP009273/1391360‑1391642

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.