Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,199,869	+GA :: IS3 (+) +4 bp	coding (935‑938/1128 nt)	intE ←	putative integrase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	315229 =	NA (NA)	35 (0.700) +TC	33/480	0.4	100%	noncoding (1/1255 nt)	IS3	repeat region
	?	NC_000913	= 1199872	0 (0.000)					coding (935/1128 nt)	intE	putative integrase
*	?	NC_000913	1094245 =	NA (NA)	21 (0.420)	21/484	0.9	100%	noncoding (1258/1258 nt)	IS3	repeat region
	?	NC_000913	1199869 =	0 (0.000)					coding (938/1128 nt)	intE	putative integrase

CGTGCGAAAGCTTTAGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATAC  >  NC_000913/1093995‑1094492                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                        cGTGCGAAAGCTTTAGCGGACCGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGTCAAATGCGTTACACCCAAATGAGATCTATCGACTAGCTGCTAACTCACTTTACGAGCCGAAAGAGACAGGGCGTAATCCGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGCGTCCACATGAAGCGGCAtttt                                                                                                                                                                                                                                                         >  2:209656/1‑251 (MQ=255)  gTGCGAAAGCTTTAGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTg                                                                                                                                                                                                                                                        >  1:52369/1‑251 (MQ=255)      gAAAGCTGTAGCTGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTAGACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGATGGATGTGGTGAATCTTTTTGAGTCACCATAAAGCTGCAGTTTGATcc                                                                                                                                                                                                                                                    <  2:412315/251‑1 (MQ=255)                 cGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCCCGTa                                                                                                                                                                                                                                          >  1:119897/1‑250 (MQ=255)                  gaaaaaggttCGGGAAAATGTTGAGCGTTTCACTGACGCTGATCCTGAATACGCTATACCAAACAAAGTAACGATTAGGATTGGCGCTGTTGTGACTCAGGCAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGAGTACTAAGGAGGTTGTGAGGGATGTGGTGCATTTTTGTGAGTCGCCATAAAGCGGCATTTGGATACTACCAACATAat                                                                                                                                                                                                                                        >  2:488840/9‑251 (MQ=255)                       ggATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAACTGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGCGACCGGGCGTACTACGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTTCCCAAGTTATATgg                                                                                                                                                                                                                                    >  2:432304/1‑250 (MQ=255)                              ggAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACAAAAAAAAGCGACGATTAGTATTGGCGCTGTTGTGACTAAGGAAACTGCGTTAAACCCAAATGAGATCTATCGACTGGCTGCTAACGCACTTTACGAGGCGAAAGCGACCGCGCGTAATAAGGAGGTGGTGAGGGATGTGGGGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGCTCATACCCACGTAATATGGacaccgtc                                                                                                                                                                                                                            >  2:383501/1‑247 (MQ=255)                                            gTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGGGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTAGCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTGTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCt                                                                                                                                                                                                              <  1:377391/251‑1 (MQ=255)                                             tttAACTGGCGATAATCCTGCATTCGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGc                                                                                                                                                                                                                      >  1:434946/1‑242 (MQ=255)                                             tttAACTGGCGATAATCCTGAATTCGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAga                                                                                                                                                                                                                      <  2:434946/242‑2 (MQ=255)                                                                  aTACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACt                                                                                                                                                                                        <  1:405052/251‑1 (MQ=255)                                                                  aTACGCGATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCATGAAAATGCGTTAAACCCAAATTAGATCTATCGACTGGCTGATAACGCACTTGACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGTTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCGTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACt                                                                                                                                                                                        <  2:234634/251‑1 (MQ=255)                                                                         ataCCACAAAAAGTGACGATTAGTATTGGCGCTGGTGTGCCTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgcc                                                                                                                                                                                  <  2:537565/250‑1 (MQ=255)                                                                           aCCACAAAAAGTGACGAGTAGTTTTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCAATCGACTGGCTGATAACGCTCTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGGGGTTGTGAGGGAGTTGGTGAATTTTTGTGAGTCCTCATAAAGCGGCATTTTGATCCTACCCACGTAATCTGGACACAGGCCTAAGCGAGGTTATTGTCTTCAAATTGTTCCGGACTCAGgccgtc                                                                                                                                                                               <  2:398390/251‑3 (MQ=255)                                                                            ccACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCca                                                                                                                                                                              <  2:15588/251‑1 (MQ=255)                                                                                        aCGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgc                                                                                                                                                                  >  1:155147/1‑251 (MQ=255)                                                                                           aTTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCACATTGTTCCGGACTGCGGCCGCCACACCAACt                                                                                                                                                                      >  2:567260/1‑244 (MQ=255)                                                                                           aTTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACt                                                                                                                                                                      <  1:567260/244‑1 (MQ=255)                                                                                               tgagtGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGacac                                                                                                                                                                                                                                <  2:116574/178‑1 (MQ=255)                                                                                               gTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGacac                                                                                                                                                                                                                                >  1:116574/1‑182 (MQ=255)                                                                                                 aTTGGCGCTGTTGTGAATCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCa                                                                                                                                                          <  1:117644/250‑1 (MQ=255)                                                                                                   tGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCAcc                                                                                                                                                        <  1:159417/250‑1 (MQ=255)                                                                                                      cgcTGATGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGAtt                                                                                                                                                    >  2:514413/1‑251 (MQ=255)                                                                                                                                     ccAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGACAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGATTTCAACTTGTTCCGGACTGAGGCCGCCACACCAACTGTACCGCCGCCCCCGATTGTAACAACTTTGGATATAATTAAACACCgat                                                                                                                     >  2:50424/1‑249 (MQ=25)                                                                                                                                                    cGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTGTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTc                                                                                                       <  1:344617/250‑1 (MQ=255)                                                                                                                                                         ggCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCt                                                                                                 >  1:483363/1‑251 (MQ=255)                                                                                                                                                                                                         ggtTGTGAGGGAAGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTACAATTTCAGCGAATGAaaga                                                  >  1:569437/1‑250 (MQ=255)                                                                                                                                                                                                             gtgAGGGATGTGGTGAATTTTTGTAAGTCCCCATAAAGCGGCATTTTGATCTGACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTGTCAATTTGTTCCGGACTTAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTGCAGCGAATGAAAGAAGCt                                              <  1:488840/250‑1 (MQ=14)                                                                                                                                                                                                                             aTTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTAt                             <  1:288359/251‑1 (MQ=255)                                                                                                                                                                                                                                                         tttGATCCTACCCACGAAATATGGACCAAGGCTGTAGGGGGGTTTTTGTTTTCAAATTGTTACGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATAc  <  2:329217/250‑1 (MQ=11)                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                        CGTGCGAAAGCTTTAGCGGAAAGGATTCGGGAAAATGTTGAGCGTTTAACTGGCGATAATCCTGAATACGCTATACCACAAAAAGTGACGATTAGTATTGGCGCTGTTGTGACTCAGGAAAATGCGTTAAACCCAAATGAGATCTATCGACTGGCTGATAACGCACTTTACGAGGCGAAAGAGACCGGGCGTAATAAGGTGGTTGTGAGGGATGTGGTGAATTTTTGTGAGTCACCATAAAGCGGCATTTTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCCGCATTATTTCCCGGCTGATAAAGTGTTCTCCATGGATACATTCCACTTTCAGCGAATGAAAGAAGCTTTCCACGCAGGCATTATCGTAGCAGCAACCTTTTGCGCTCATAC  >  NC_000913/1093995‑1094492

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ 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.