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 (0.810) +TCAATT	15/266	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

AAAATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/62679‑62817 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATT  >  USA300TCH1516_ALE/62818‑62946                                                                                                                                            ||||||                                                                                                                                  AAAATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTC                                                                                                                                       >  1:162213/1‑141       GAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAAGATGCTCTCAATTTg                                                                                                                                 >  2:74282/1‑140                AAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTAACGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTG                                                                                                                        <  2:132652/141‑1                     ACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATT                                                                                                                   <  1:94707/141‑1                          AACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATAT                                                                                                              >  2:64992/1‑141                                   TACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGCGCATCCTTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCAT                                                                                                     >  2:193547/1‑141                                   TACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTGAAATAAGCTTCAT                                                                                                     >  2:142149/1‑141                                   TACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCAT                                                                                                     <  2:62893/141‑1                                    ACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATT                                                                                                    <  1:39334/141‑1                                                GTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGT                                                                                        >  1:154180/1‑141                                                      GTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAA                                                                                  <  2:10857/141‑1                                                                   CGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAA                                                                     >  1:162906/1‑141                                                                                        AATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGT                                                >  1:227874/1‑141                                                                                                          gacAGCACCCCTTACCGCAAAGTGAATGACGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCAT                              <  1:17978/138‑1                                                                                                                         CGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTAGTACGTCATCATTCATAAAATCCTCGTAGAT               >  1:64486/1‑141                                                                                                                                    GGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAA    <  2:162213/141‑1                                                                                                                                      ATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATT  <  1:236970/141‑1                                                                                                                                            ||||||                                                                                                                                  AAAATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/62679‑62817 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATT  >  USA300TCH1516_ALE/62818‑62946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.