New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1397238	NA (NA)	21 (0.680)	20/490	0.5	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	NC_000913	= 1978494	0 (0.000)					intergenic (‑297/+24)	flhD/insB5	DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB

CGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATCGGCGGCGTTATAGAACAGTAC  >  NC_000913/1397022‑1397487                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                          cGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAACTGATACGTCCGTGGGAGAGATCCCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTAAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCCATGCGTTGATTGTAAATcacgct                                                                                                                                                                                                                         >  1:306725/1‑246 (MQ=255)            aCGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGCGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTAAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAgaggtgagg                                                                                                                                                                                                              >  1:113952/1‑251 (MQ=255)                  gCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGCGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTCAATCCAGCTAAGAGGTGAGGCTTTc                                                                                                                                                                                                         >  1:17285/1‑250 (MQ=255)                            ttCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTGCAGAGCAGACa                                                                                                                                                                                               <  1:235366/250‑1 (MQ=255)                             tCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGGCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAAGCAATGCGTTGATTGTAAATCCAGCTAAGAGGGGAGGTTTTCAGAGCAGACaa                                                                                                                                                                                              <  2:259386/250‑1 (MQ=255)                              cgtgCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGTCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAATAAAGGAAATGACTGAGTCATCCGAGAATAATGTCCCCGCTGATGCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCATCTAAGAGGTGAGGTTTTCAGAGCAGACAACg                                                                                                                                                                                            <  1:178269/248‑1 (MQ=17)                                                    aGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATGCGCACCTTCCCTAACGAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTTAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTa                                                                                                                                                                      <  1:269601/251‑1 (MQ=255)                                                                          aCTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAAGCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCTCTTATTCGCACCGTCCCGAACTAATCAATGCGGTGATTGTAAATCCAGCTAATAGGTGAGGTTTTCAGAGCAGGCAACGGTGAAATGTTATGGTATTGTTGGGTTGAGGTAACAAGAAATTTg                                                                                                                                                <  2:53219/251‑1 (MQ=18)                                                                                                               aaaTAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAAc                                                                                                             <  1:43962/249‑1 (MQ=255)                                                                                                                                    ttACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTTCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGgaagaa                                                                                       <  1:128500/250‑1 (MQ=255)                                                                                                                                                aaaTCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTTTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTTAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGt                                                                          <  1:273382/251‑1 (MQ=255)                                                                                                                                                 aagcGGCGCAAACATGAAGAAATGAAATGACTGAGTCAGCCTAGAAGAATTTCCCCGATTAGTCGCACCTGCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAATAGGTGAGGTGTTCATAGCAGACAACGGTGAAATGTCATGGTATGGTTACGTGTAGGTAACAAGAAATGTGACAGCACAAGGATTACATCATGATTTTGGCGAAACGGAATTCAGCGAAAGGGAAGAAATGTCTCTTTAGtt                                                                         <  2:306725/248‑1 (MQ=255)                                                                                                                                                 aaTCGGCTCAAACATGAAGAACTGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATCGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGTAATTTCTCTTTGGtt                                                                         >  2:120631/1‑251 (MQ=255)                                                                                                                                                         aaaaCAAGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATGCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATTGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATGATGGCGAAACTGAAGGCAGCGAAAGGgaatatagaactcttgtgtgcgttggc                                                                  <  2:210283/249‑25 (MQ=38)                                                                                                                                                             cATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGGAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGttt                                                             <  2:157038/251‑1 (MQ=255)                                                                                                                                                                 aagaaATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCat                                                         <  1:76012/251‑1 (MQ=255)                                                                                                                                                                     aatgaaatgaCGGAGTCAGCCGAGAAGAATTTCCCCTCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGAGTGTAAATCCAGCGAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGTTATGGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGGAATTTCTCTTGGGTTTGTTTGCGGTTTGCattatt                                                     <  2:305579/251‑1 (MQ=255)                                                                                                                                                                          aatgaCTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTGTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCGGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTgcggc                                                <  1:293837/251‑1 (MQ=255)                                                                                                                                                                                 gAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCgg                                           <  1:39079/249‑1 (MQ=255)                                                                                                                                                                                             aagaaTTGCCCCGTTTCTTTGCCCCATCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTTAAATGTCTTGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATAATTATGGCGAAACTGAAGTCATCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTTCGACGTCGGTtgtgtcacgcact                             <  2:156276/251‑10 (MQ=255)                                                                                                                                                                                              agaaTTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGGTGATTGTAAATCCAGCTAAGAGGCGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGACGGTTGTGACTcgcgcg                             >  1:302248/1‑250 (MQ=255)                                                                                                                                                                                                aaTTTCCCCGCTTAGTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGATTTCAGAGAAGACAACGGTGCAATGTCATGGTATTGTTACGTTTAGGGAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAACCTGAAGTCAGCGAAAGGGAAGCAATTTATCTTTGGTTTGTTGGCGGGTTTCCTTGTTGACGCGTCGGTGGTGaactcatcgagc                          >  2:174071/1‑240 (MQ=255)                                                                                                                                                                                                 aTTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGCCATGGTATTGTTACGTATAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGAGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGAcc                          >  1:133153/1‑250 (MQ=255)                                                                                                                                                                                                        cGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATcggcgg                  >  1:69531/1‑251 (MQ=255)                                                                                                                                                                                                            tATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTGTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAGTTGGCTCTTTGGTTTGTTGGCGGTGTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATCGGCGGCGt               <  1:297514/250‑1 (MQ=255)                                                                                                                                                                                                             aTTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGTAGAAATTTCTCTTTGGTTTGGTGGCGGTTTTCATTATTGGGGTGTCGGTTGTGATTCGCGCGTTCATGGGCGGCGtt              <  2:137449/250‑1 (MQ=255)                                                                                                                                                                                                             aTTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATcg                      <  2:120286/242‑1 (MQ=255)                                                                                                                                                                                                             aTTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATcg                      >  1:120286/1‑242 (MQ=255)                                                                                                                                                                                                                    ccTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGCGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCAt                        >  1:109980/1‑233 (MQ=255)                                                                                                                                                                                                                    ccTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCAt                        <  2:109980/233‑1 (MQ=255)                                                                                                                                                                                                                         ccTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGAGAGGTTTTCAGAGCAGAAACCGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAGACTGAAGTAAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCGTTATTTCGGCATCGGTTGGTACTCGCGCGAccgtatgcggagtttaagaacggtaa  >  1:306247/1‑226 (MQ=255)                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                          CGATGTTATTCACGCTGGCCAACCTGTTTCGGGCGGACCAAATGATACGTCAGTGGGAGAGATCTCACTAAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAACTAATCAATGCGTTGATTGTAAATCCAGCTAAGAGGTGAGGTTTTCAGAGCAGACAACGGTGAAATGTCATGGTATTGTTACGTTTAGGTAACAAGAAATTTGTCTGCACAAGGATTACATCATGATTATGGCGAAACTGAAGTCAGCGAAAGGGAAGAAATTTCTCTTTGGTTTGTTGGCGGTTTTCATTATTGCGGCGTCGGTTGTGACTCGCGCGACCATCGGCGGCGTTATAGAACAGTAC  >  NC_000913/1397022‑1397487

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ 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.