Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	3,807,520	IS1 (–) +8 bp	coding (572‑579/1035 nt)	waaQ ←	lipopolysaccharide core heptosyltransferase 3

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	3583428 =	NA (NA)	59 (1.280)	55/476	0.1	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	3807520 =	0 (0.000)					coding (579/1035 nt)	waaQ	lipopolysaccharide core heptosyltransferase 3
*	?	NC_000913	= 3584195	NA (NA)	74 (1.610)	67/476	0.0	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	= 3807527	0 (0.000)					coding (572/1035 nt)	waaQ	lipopolysaccharide core heptosyltransferase 3

GACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTATGGAAAAACTTACAACGGAACTACACTCCTTAAGTGAGATG  >  NC_000913/3583956‑3584445                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                           gACGTGGTGATATGGATGACGGATGGCTGGCCGCGGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAAGCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTGCCGACATTaaaa                                                                                                                                                                                                                                                  <  2:263019/250‑1 (MQ=18)      ggtgATATGGATGACGGATGGCTGGCCGCTTTATGAAACCTGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCTCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCAGTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACt                                                                                                                                                                                                                                            <  2:206102/251‑1 (MQ=255)         gtaatggtggacggtgggttggacGCTGTATAAACCCCGCCTGAAGTGAAAGCTGCCGGTAATCAGCAAGCGATATACGCAGCGAATTGAGCCGCTTAACCGGAATCGGAGGCAGCACCTGGCACGGCTTGGACGGAAGTCGCTTTCGTTCTCAAAATCGGTGGAGCTGCAGGCCAAAGTCATCGGGCATTAGCTGAACATATAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACttgt                                                                                                                                                                                                                                         <  2:363617/228‑3 (MQ=11)             tGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGCATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACCTTAAAAGAAACTTTTTTg                                                                                                                                                                                                                                      >  2:255687/1‑250 (MQ=25)                aTGACGGAGGACTGGCCGCTGGATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAAGCGGTGGAGCTGCATGAAAAAGTAATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTGTTTTGAAAt                                                                                                                                                                                                                                  <  2:13167/251‑1 (MQ=14)                                    gTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGcac                                                                                                                                                                                                                >  2:135585/1‑249 (MQ=255)                                        gAATCCCGCCGGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGaaaa                                                                                                                                                                                                          <  2:132552/251‑1 (MQ=255)                                          aTCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCTCCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAata                                                                                                                                                                                                        <  2:391403/251‑1 (MQ=255)                                           tCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGAACGGATGGGACGGAAGTCGCTGTAGTTCTCAAAATCGGTGGAGCAGCATGACAAAGTCATCGGGCAGTATCTGAACATAAAACACTATCAATAAGTTGGAGTAATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAatat                                                                                                                                                                                                       >  2:360213/1‑251 (MQ=255)                                            cccGCCTGAAGGGAAAGCTGCCCGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCGGGCACGGTTGGGACGGAAGTCGCTGTCGTTCTTAAAATCTGTGGAGCTGCAGGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTGGGAGTCATTACCGACAGTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAatata                                                                                                                                                                                                      <  1:310292/251‑1 (MQ=17)                                               gCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTc                                                                                                                                                                                                   <  1:20666/251‑1 (MQ=255)                                                ccTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCGGGGACGGAAGTCGCTGTCGTTCTCAAAAGCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGGCATGACCGACATTAAAAGTAACTTTTTTGAAATTAGAGAGAATATTGGCACAGAAAATAGATTCa                                                                                                                                                                                                  <  2:217570/251‑1 (MQ=255)                                                   gAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGAGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAAAACTATCATTAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAACATATATTCAGtt                                                                                                                                                                                               >  2:111890/1‑251 (MQ=255)                                                    aaGGGAAAGCTGCACGTAATAAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTc                                                                                                                                                                                              <  2:270712/251‑1 (MQ=255)                                                      gggAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCGGTTCGt                                                                                                                                                                                            <  1:130633/251‑1 (MQ=255)                                                               gCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGAt                                                                                                                                                                                    <  1:278485/250‑1 (MQ=255)                                                                  cGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTtct                                                                                                                                                                                <  1:31629/251‑1 (MQ=255)                                                                         aGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGCCGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAt                                                                                                                                                                                                                                                       >  1:387604/1‑173 (MQ=17)                                                                         aGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACAt                                                                                                                                                                                                                                                       <  2:387604/173‑1 (MQ=32)                                                                         aGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCAtt                                                                                                                                                                         >  1:156276/1‑251 (MQ=255)                                                                                       gCAGCGAATTGAGCCGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGATGTCGTTCTCAAAATCGGAGGAACTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACCTTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATc                                                                                                                                                            >  2:456847/1‑250 (MQ=255)                                                                                          gCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATgg                                                                                                                                                        >  1:302841/1‑251 (MQ=255)                                                                                                                                     cGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTaa                                                                                                             <  1:455267/251‑1 (MQ=255)                                                                                                                                       gCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAAc                                                                                                           <  2:302841/251‑1 (MQ=255)                                                                                                                                          gggACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAt                                                                                                        <  1:343647/251‑1 (MQ=255)                                                                                                                                                                 cAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACcag                                                                                 <  2:117435/251‑1 (MQ=255)                                                                                                                                                                            gAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTcc                                                                      <  2:156276/251‑1 (MQ=255)                                                                                                                                                                                 gCATGACAAAGACATCGGGCATTATCTGAACATACAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGtt                                                                 >  2:297132/1‑251 (MQ=255)                                                                                                                                                                                                        aTCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTAt                                          >  1:30456/1‑251 (MQ=255)                                                                                                                                                                                                                          aTCAATACGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTAAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATAATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTATGGAAAAACTTACAACgg                         >  2:175510/1‑250 (MQ=255)                                                                                                                                                                                                                                               ccGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTATGGAAAAACTTACAACGGAACTACACTCCTTAAATGAGAt   <  1:135585/251‑1 (MQ=255)                                                                                                                                                                                                                                                cGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTGCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAAGTCCTTGTTCGAAATTTAGCAGTGCAAGCTATGGAAAAACTTACAACGGAACTACACGCCTTAAGTGAGATg  <  2:199906/251‑1 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                                           GACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCCCGCCTGAAGGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCATGCCATCTTTTTAGAGATTACCAGCAGAAAATTCCTTGTTCGAAATTTAGCAGTGCAAGCTATGGAAAAACTTACAACGGAACTACACTCCTTAAGTGAGATG  >  NC_000913/3583956‑3584445

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ 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.