Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	USA300TCH1516_ALE	62,818	+CAATTT	intergenic (‑285/+228)	USA300TCH1516_00053 ← / ← speG	hypothetical protein/Spermidine N(1)‑acetyltransferase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 62817	0 (0.000)	16 (0.830) +TCAATT	14/266	0.3	100%	intergenic (‑284/+229)	USA300TCH1516_00053/speG	hypothetical protein/Spermidine N(1)‑acetyltransferase
	?	USA300TCH1516_ALE	62818 =	0 (0.000)					intergenic (‑285/+228)	USA300TCH1516_00053/speG	hypothetical protein/Spermidine N(1)‑acetyltransferase

AATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/62686‑62817 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTC  >  USA300TCH1516_ALE/62818‑62951                                                                                                                                     ||||||                                                                                                                                       AATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTAT                                                                                                                                     <  2:222767/141‑1    TATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTT                                                                                                                                  <  2:80329/141‑1               CGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTA                                                                                                                       >  1:70684/1‑141                   AACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATAT                                                                                                                   >  2:132026/1‑141                     CAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAA                                                                                                                 <  1:165520/141‑1                                 ctAAAAATGTTTGTGTAATTCTGCGAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGA                                                                                                     <  1:105460/139‑1                                 CAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGA                                                                                                     <  2:120245/141‑1                                 CAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGA                                                                                                     <  2:191785/141‑1                                       attTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCACTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGATTCATTCTGATAGATA                                                                                               <  2:13001/138‑1                                                       GATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTT                                                                               <  2:123951/141‑1                                                                                AAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTG                                                      <  2:12060/141‑1                                                                                               AATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCAT                                       >  2:83620/1‑141                                                                                                    AGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATA                                  <  2:216085/141‑1                                                                                                    AGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATA                                  <  2:102887/141‑1                                                                                                     GAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAA                                 <  1:18885/141‑1                                                                                                            CCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTC                          >  1:146292/1‑141                                                                                                                                    CTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTC  >  2:30514/1‑141                                                                                                                                    CTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTC  >  2:70918/1‑141                                                                                                                                     ||||||                                                                                                                                       AATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/62686‑62817 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTC  >  USA300TCH1516_ALE/62818‑62951

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ 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.