Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	295,738	IS2 (–) +5 bp	coding (1355‑1359/1401 nt)	intF ←	putative phage integrase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	295738 =	1 (0.030)	47 (1.160)	44/496	0.1	97.9%	coding (1359/1401 nt)	intF	putative phage integrase
	?	NC_000913	381260 =	NA (NA)					noncoding (1/1331 nt)	IS2	repeat region
*	?	NC_000913	= 295742	1 (0.030)	42 (1.030)	39/496	0.2	97.6%	coding (1355/1401 nt)	intF	putative phage integrase
	?	NC_000913	= 382590	NA (NA)					noncoding (1331/1331 nt)	IS2	repeat region

GTAGCGATAATTCCCTCTGGAGTTCGAACAGACACGGGCTGTTCATCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAGCAA  >  NC_000913/381025‑381506                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                       gTAGCGATAATTCCCTCTGGAGTTCGAACAGACACGGGCTGTTCATCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTg                                                                                                                                                                                                                                          >  2:319806/1‑250 (MQ=255)         aaTTCCCTCTGGAGTTCGAACAGACACGGGCTGTTCATCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCa                                                                                                                                                                                                                                  <  1:355114/250‑1 (MQ=255)          aTTCCATCTGGAGTTCGAACAGAAACGGGCTGATCATCCCGACGATGAATACAGGGACGTACTTGTGCGCCTAAATATGCTAGGGTTACAATTACTGAGTCGGCAATCAAA‑CATTGCGGAACATTCGTTACTTACGCTTCAATAAACGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTcc                                                                                                                                                                                                                                   >  1:375480/1‑248 (MQ=255)                                        tGTTCATCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGAGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTc                                                                                                                                                                                                  >  2:96114/1‑251 (MQ=255)                                               gcagacgtttattgattggaaattcTTGTGTGCCTAAGTCTGCCTGATATGCACCTCCCTAGTCGACAATATAT‑CATTGTGGACGAATCTTTTCTGCCTCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAAGACGAATAAACG‑CATAATTACTAGACTGGCCTCCTGAATATCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATAc                                                                                                                                                                                           <  2:35465/227‑1 (MQ=19)                                                    cGATGATTACTGGTACGTACATGTGCGCCTAAATATGCCTGGTGTGCAACTACCGAGTAGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATGTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATAGCACTTAAATAAGTGATAGTCTTAATACTAGtt                                                                                                                                                                                      <  2:28496/251‑1 (MQ=255)                                                               ggTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGAAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGAAAACCAATATCACTTAAATCAGTGATAGTCTTAATACTAGTTTTTAGACTAGt                                                                                                                                                                           >  1:357731/1‑251 (MQ=255)                                                                    gtacTTGTCAGCCTAAATATGCCGGGTTTGCAACTACAGCGTCGGCAATAAAA‑AATAGCGGACCAATCGTTGCTTCCGCTTAAATCACCGCATTTTTAATCTCGGTGGCAAAACCCATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGAAAACAAATATCACTTAAATAAGTGAAAGTCTTAATACTAGTTTTTAGACTAGTCATTg                                                                                                                                                                      >  2:157903/1‑251 (MQ=37)                                                                                   aaTATGACTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattg                                                                                                                                                       <  2:356732/251‑1 (MQ=255)                                                                                     tatGCCTGGTTTGCAACTACCGAGTCGTCAATAAAAGCAT‑GCGGACCACAAGCTGCTTCCGCTTCAATAACCGCATTTTTAATCCCGGTGGCAACACCCATATTTCCGCCATTCCTGATTATT‑GCGCCAGGACGAATAAACG‑CATAATTACTAGACTAGCCCCCTGAATCACCAGACAACCCATATCACTTAAATAAGAGATAGTCTTAATACTAGTTTTTAGACTAGTAATTGGAGAACAGAtgattgat                                                                                                                                                     >  1:195331/1‑251 (MQ=21)                                                                                      atGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGAtgattgat                                                                                                                                                     <  1:96114/250‑1 (MQ=255)                                                                                           tGGTTTGCAACTACCGCGTCGGCAATAAAA‑CATTCCGGACTAATTGTTGCCTCCGCTTCAATACCCGCATTTTTAACCTCGGTGGCAACAACAATTTTTACGCCATTGCTGATTATT‑GTTACAGGACGAATCTACC‑CATATTTACTAGACTGGCCCCCTAAATCTCCCGACCACACCTATCACTTAAATAATTGATAGTCTTAATCCTCGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGCCtt                                                                                                                                                >  2:165132/1‑250 (MQ=19)                                                                                                              cGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGAc                                                                                                                            >  1:230745/1‑251 (MQ=255)                                                                                                              cGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGAc                                                                                                                            <  1:322340/251‑1 (MQ=255)                                                                                                                 aaaTAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGc                                                                                                                         <  2:315269/250‑1 (MQ=255)                                                                                                                      aaa‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTAcc                                                                                                                    <  1:426456/251‑1 (MQ=255)                                                                                                                               aggaaccaagggtGCTTCCACTTCAAAAACCGCATTTTTAATCCCGGGGGGAAAACCAAATTTTTCGCCATTTCCGAATATTTGGGCC‑GGACGAATAAACGGAATAATT‑CTAGACTGGCCCCCCTAATCTCCAGACAACCAATAACTATTAAATAAAGGATAGGCTTAATTCCAGGTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTATGGCCGGAGAAACGCAGACGTCGTACCACACAGGa                                                                                                            <  2:338245/239‑1 (MQ=9)                                                                                                                                    cAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTGGGTTGCAAAATCAATTTTTACGCCATTGCTGATTATT‑GTTCCAGGACGAATAAACG‑CATAATTACTATACTGTCCTCCTGGATCACCAGACGACCAATATCACTTAAATAAGTGAGAGTTTTCATACTTGTTTTTAGATTAGTCATTGGAGAACAGATGAGTGGTGGCTTAGTGCCGGAGAATCGCAGACGGCGTTCCACACTGTAAAAGa                                                                                                       <  2:165239/251‑1 (MQ=255)                                                                                                                                          ttGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCACAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATCATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGTAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCa                                                                                                  >  2:57317/1‑250 (MQ=255)                                                                                                                                                         tAACCGAATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTTGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCt                                                                                  >  1:266468/1‑251 (MQ=255)                                                                                                                                                           aCCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCttt                                                                                <  1:183893/251‑1 (MQ=255)                                                                                                                                                            ccGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTg                                                                               >  1:69511/1‑251 (MQ=255)                                                                                                                                                                aTTTTTGATATCGGAGGCAAACACAATTTTTACGCAATTGAAGATTATT‑GTACCCGGCCCAAAAAACA‑CATAATTACTCAACTCTCCCCCTAAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTATTAATACTAGTTTTTAGACTAGTCATTGGGGCACACATGATTGATGTCTTCGGACAGGCGAAACGAAGACTGCGCACACCACAGGCAAAGATCGAAATTATTAAGAAGAGCTTTGCAcc                                                                           >  2:414492/1‑251 (MQ=2)                                                                                                                                                                         ctcGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGAc                                                                  >  1:140222/1‑251 (MQ=255)                                                                                                                                                                                                        gctgattaaagtgcaaaaacgaataaacg‑aataaTTAATAGACTGGAACCCTGAATCTCCAGCCAAACCCTATCACTTAAATAAGAGATAGTCTTAATACTAGTTTTTAGACTAGTAATTGGAGAACCGATGATTGATGTCTTAGGACCGGCAAAACGCAGACGGCGTACCACACCGGAAAAGATAGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGgtgt                                    >  2:429644/19‑251 (MQ=11)                                                                                                                                                                                                             ttgatatgcaaGGACGAATAAAAG‑AATAATTACTAGCCTGGCCGCCTGACACCCAAGAACACCCCTATAACTTAAATAAGACATCGTGATAAAACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGCTCTCTTAGGTACGGAGATACGTCGCCACCCGACCACACAGCCCAAGCTCGCAATTGTTCAGCAGAGCTTTGAACCGGCAATGACGGACTCCCTCGTTGCCAGTCAACATGGTGTagc                                 >  2:70357/11‑249 (MQ=2)                                                                                                                                                                                                                         gACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTAt                   >  2:343740/1‑251 (MQ=38)                                                                                                                                                                                                                                         aaTTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAg     <  1:297955/250‑1 (MQ=31)                                                                                                                                                                                                                                           ttACTAGACTGGCCCCCTGAATCTCCAGACAAACAATATCACTTAACTAAGTGATAGTCTTAATACTAGTTTTTAGACTACTCATTGGAGAACAGAAGATTGATGTCTTAGGGCCGGAGAAAAGCAGACAGCGTACCACACAGGAAAAGATCGCAATTGTTACGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAGCa   >  1:437733/1‑250 (MQ=11)                                                                                                                                                                                                                                            tACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTATGTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAGCaa  <  2:306944/250‑1 (MQ=11)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                                       GTAGCGATAATTCCCTCTGGAGTTCGAACAGACACGGGCTGTTCATCCAGACGATGATTACTGGTACGTACTTGTGCGCCTAAATATGCCTGGTTTGCAACTACCGAGTCGGCAATAAAA‑CATTGCGGACCAATCGTTGCTTCCGCTTCAATAACCGCATTTTTAATCTCGGTGGCAAAACCAATTTTTACGCCATTGCTGATTATT‑GTGCCAGGACGAATAAACG‑CATAATTACTAGACTGGCCCCCTGAATCTCCAGACAACCAATATCACTTAAATAAGTGATAGTCTTAATACTAGTTTTTAGACTAGTCATTGGAGAACAGATGATTGATGTCTTAGGGCCGGAGAAACGCAGACGGCGTACCACACAGGAAAAGATCGCAATTGTTCAGCAGAGCTTTGAACCGGGGATGACGGTCTCCCTCGTTGCCCGGCAACATGGTGTAGCAGCCAGCCAGTTATTTCTCTGGCGTAAGCAA  >  NC_000913/381025‑381506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 29 ≤ 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.