New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 609351	NA (NA)	6 (0.300)	6/256	NT	35.3%	noncoding (1345/1345 nt)	IS186	repeat region
	?	NC_000913	2227427 =	11 (0.550)					pseudogene (1332/1436 nt)	mdtQ	putative multidrug resistance outer membrane protein MdtQ

GCTTACAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTACCAGATGTTGTCAATTAATCGTGTTGGCACAGCGTTATGACTATCTTTT  >  NC_000913/609213‑609493                                                                                                                                           |                                                                                                                                               gCTTACAGGGGGTCAGTCGTGGGACAGTACCCCTGACCGCCTACAAAACGCAATTGAAGTACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTaa                                                                                                                                            <  2:331549/143‑1 (MQ=11)     aCAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATccc                                                                                                                                        <  1:301185/143‑1 (MQ=35)                  cGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGtt                                                                                                                           <  1:97280/143‑1 (MQ=255)                  cGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTGAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGtt                                                                                                                           <  1:213334/143‑1 (MQ=255)                      ggACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTgtca                                                                                                                       <  1:368353/143‑1 (MQ=255)                            tATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGGTgtcaggtcgg                                                                                                                 >  1:275698/1‑141 (MQ=255)                                ccTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATg                                                                                                             >  1:269177/1‑143 (MQ=255)                                           tcataatgCAATTGAAGAACTCGATGCATCGTCTTAACGAGGCACCGATTCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCt                                                                                                  <  2:203408/136‑1 (MQ=21)                                                 cGCAATTGAAGATCGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAATCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTa                                                                                            <  1:209000/143‑1 (MQ=255)                                                          agaaCGCGCGGCATCGTCGGAGCGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAGCCCTTAAGTTAGCGTTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGc                                                                                   <  2:63069/143‑1 (MQ=25)                                                          agaaCGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTCTGGGCGTGTACCCCTCATAGCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGc                                                                                   >  1:394582/1‑143 (MQ=21)                                                             aagcgAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCATTACACTTTCGCCCg                                                                                >  2:9150/3‑143 (MQ=255)                                                                 gAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGt                                                                            >  2:12309/1‑143 (MQ=255)                                                                       gcgtcgtAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGa                                                                      <  2:124437/142‑1 (MQ=255)                                                                            ttAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCt                                                                 >  2:325502/1‑143 (MQ=255)                                                                                 gAGGCACCGAGGCGTCGCATTATTCAGATGGTACAAACCTTAAGAAAGAGCTTATGGGAGTAATAGCCGCATATCCGGTTGTCAGGACAGGACAGTAAGGCACCTGCTTTACACTTCCGCCCGTGGAACGAGATGGCAGCgcg                                                            >  2:27709/1‑141 (MQ=21)                                                                                       ccGAGGCGGCGCAAGCTTCAGATGGTGCAACCCTCAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATc                                                      <  1:350804/143‑1 (MQ=255)                                                                                           ggCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTAc                                                  >  1:298244/1‑143 (MQ=255)                                                                                                       ttcatttGGTTTAACTCTTAAGTTATCGCATATGGGAGTAATCCCCGCATATCAGGTTATCACGTCTGGATGCTAAGTCACCTGCTTTAAACTTTCGCCGGTGGTCTGAGATGAACGCGGGCGAGTCGTACGGGCTGTTGTcc                                      >  2:66430/7‑142 (MQ=255)                                                                                                        tcAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATTCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTGCACCGTGGTCAGTGATGGCTGAGTGCGAATTGTAGCAGGTGGTGTGaa                                     >  2:343101/1‑143 (MQ=37)                                                                                                                   aaCCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACATGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTACCAGACGTTGTCAATTAAGCGCGtt                          >  2:221341/1‑143 (MQ=255)                                                                                                                     cccTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTACCCGATGTTGTCAATTAATCGTGTTgc                        >  1:377553/1‑142 (MQ=255)                                                                                                                                 cgcTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTACCAGATGTTGTCAATTAATCGTGTTGGCACAGCGTTATg            >  2:50194/1‑143 (MQ=255)                                                                                                                                    ttATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTACCAGATGTTGTCAATTAATCGTGTTGGCACAGCGTTATGACt         >  1:227428/1‑143 (MQ=255)                                                                                                                                           aGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCACTGCTGCCTGCGGACGAATCGTACCAGATGTTGTCAAGTCATCGTGTTGGCACAGCGGTATGACTAtctgta  >  2:300833/1‑140 (MQ=255)                                                                                                                                           |                                                                                                                                               GCTTACAGGTGGCCATTCGTGGGACAGTATCCCTGACAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCAGATGGTTCAACCCTTAAGTTAGCGCTTATGGGAGTAATCCCCGCATATCCGGTTGTCAGGTCAGGATGGTAAGGCACCTGCTTTACACTTTCGCCCGTGGTCAGTGATGGCTGCGGGCGAATCGTACCAGATGTTGTCAATTAATCGTGTTGGCACAGCGTTATGACTATCTTTT  >  NC_000913/609213‑609493

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.