New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	= 1391495	NA (NA)	4 (0.200)	4/276	NT	33.3%	intergenic (+146/‑127)	insH1/ynaJ	IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein
	?	CP009273	= 1972751	8 (0.390)					intergenic (‑297/‑483)	flhD/uspC	flagellar class II regulon transcriptional activator, with FlhC/universal stress protein

TGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCA  >  CP009273/1391354‑1391622                                                                                                                                              |                                                                                                                                tGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTGCCCGCTTATTCGCACCTTCCctaacta                                                                                                                          >  2:249267/1‑149 (MQ=14) tGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCctaacta                                                                                                                          >  1:211879/1‑149 (MQ=31)               tcaaTGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAt                                                                                                            >  1:201428/3‑149 (MQ=255)               tAACTGACGAAGAAACGGTCTAAATAGGATGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTGCCCGCTTAGTCGCACCTTCCCTAACTAATTAATGCGTTGAt                                                                                                            >  1:201427/1‑149 (MQ=14)               tAAATGGCGAAGAAACGGTCTAAAGAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAt                                                                                                            <  2:119320/149‑1 (MQ=255)                      cGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAAt                                                                                                     >  1:179865/1‑149 (MQ=255)                        aagaaACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATcc                                                                                                   >  1:333037/1‑149 (MQ=255)                           aaaCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGc                                                                                                >  2:307002/1‑149 (MQ=255)                           aaaCGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATACGTTGATTGCAAATCCAGc                                                                                                >  1:224675/1‑149 (MQ=255)                                   tAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgaggt                                                                                        >  1:288930/1‑149 (MQ=255)                                        aGGCTGATTCAAGGCAGTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCACACCTTCCCTAACTATTCAATGCGTTGATTGTAAATCCAGCTAAgaggtgaggt                                                                                   <  1:19451/149‑1 (MQ=255)                                                         ttACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACg                                                                  <  2:318082/149‑1 (MQ=255)                                                              ggAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGaa                                                             >  2:302329/1‑149 (MQ=255)                                                                   aaaaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCCCCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGGAGACAAGGGGGAAAGGTc                                                        >  2:141618/1‑149 (MQ=21)                                                                      aaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATg                                                     <  1:341868/149‑1 (MQ=255)                                                                           gCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTAtt                                                >  1:144383/1‑149 (MQ=255)                                                                            cTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTg                                               >  1:155549/1‑149 (MQ=255)                                                                                 aCATGAAGAAATGAAATGACTGAGTCAGCCGAGAAAAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGAGAAATGTCATGGTATTGTTACg                                          >  1:222593/1‑149 (MQ=255)                                                                                      aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTat                                     <  2:333037/149‑2 (MQ=255)                                                                                      aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                     <  2:142873/149‑1 (MQ=255)                                                                                      aagaaACGACATGACTGAGGCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAg                                     <  1:296924/149‑1 (MQ=255)                                                                                       agaaATGAAATGACTGAGTCAGCTGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAAAGGTGAGCTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAgg                                    <  1:224589/149‑1 (MQ=255)                                                                                          aatgaaatgaCTGAGCCAGCCGATAAGAATTTCCCCGCTTATTTGCACCTTCCCTAACTAAGCAATGCGTTTATTGTAAATCCAGCTAAGAGGTGAGATGTTAAGAGCAGACAACGGTGAAATGTCATGGTAGTGTGACGTATGGGTaa                                 >  1:8260/1‑149 (MQ=25)                                                                                             gaaatgaCTGAGTCAGCCGAGAAAAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACaa                              <  1:224005/149‑1 (MQ=255)                                                                                               aatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTTATGGTATTGTTACGTTTAGGTAACAAGa                            <  2:201427/149‑1 (MQ=255)                                                                                               aatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAagaaga                            >  1:250045/1‑149 (MQ=255)                                                                                               aatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGa                            <  2:201428/149‑1 (MQ=255)                                                                                                      gAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGt                     <  2:211879/149‑1 (MQ=255)                                                                                                      gAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGt                     <  1:249267/149‑1 (MQ=255)                                                                                                         tCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTg                  <  2:288930/149‑1 (MQ=255)                                                                                                                   agaaTTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGAtt        <  2:144383/149‑1 (MQ=255)                                                                                                                         tCCCCTCTTATTCGCACCTGCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGATGTGGGGTTTGCAGAGCAGACAACGGTGGAAGGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTAcatca  <  1:58642/149‑1 (MQ=255)                                                                                                                         tCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTAcatca  >  2:107500/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                TGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCA  >  CP009273/1391354‑1391622

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