Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	68,656	Δ3 bp	5.4%	coding (772‑774/852 nt)	USA300TCH1516_00061 →	hypothetical protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	68659 =	57 (0.750)	3 (0.050)	3/224	NT	5.4%	coding (775/852 nt)	USA300TCH1516_00061	hypothetical protein
	?	USA300TCH1516_ALE	= 68655	57 (0.880)					coding (771/852 nt)	USA300TCH1516_00061	hypothetical protein

AATTACCTTTATAAACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/68816‑68659 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attattattattattattGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  USA300TCH1516_ALE/68655‑68523                                                                                                                                                                                                                                                                                                     AATTACCTTTATAAACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGA                                                                                                                                                        >  1:865647/1‑141   TTAACTTTATAAACAAAAGAGCCTATAAGCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATT                                                                                                                                                      <  1:405052/141‑1                CAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAACCACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGTTAAGTGGCCTAGGTTTTGTTGACTTCGATTTTTCTTATTATTA                                                                                                                                         >  1:40525/1‑141                CAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGACTTCGATTATTATTATTATTA                                                                                                                                         >  1:282856/1‑141                CAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         >  1:278539/1‑141                CAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTA                                                                                                                                         >  1:846538/1‑141                 aaaatgGCCTATAAGCCCAGGGCACTGAACCCTTAAAACGGGAACTTAATAAACACGCCATGTTCTAGGCTATTATTTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATACGATTATGATTATTATTAT                                                                                                                                        <  2:786672/135‑1                 AAAAGAGCGTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTATTTTTTGAATTCGATTATTATTATTATTAT                                                                                                                                        <  2:602254/141‑1                                 CTAGGGCACTTAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTTTTTCTAATGTACTT                                                                                                                        <  2:618117/141‑1                                                                           CATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTC                                                                              <  1:238835/141‑1                                                                                                    TATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGAC                                                     >  2:896026/1‑141                                                                                                                                             ATTATTATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGC            >  2:375269/1‑141                                                                                                                                                  TATTATTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTG       >  1:158120/1‑141                                                                                                                                                       TTATTATTGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  2:452619/141‑1                                                                                                                                                                                                                                                                                                     AATTACCTTTATAAACAAAAGAGCCTATAATCCTAGGGCACTGAACCCTTAAAACGGGAACTTAATAAAAACACCATGTTCTAGGCTATTAATTCTCTGTATTTTACAGGGGATAAGTAGCCTAGTTTTTGTTGAATTCGATTATTATTATTATTATT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/68816‑68659 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑attattattattattattGTTTTTAATGTACTTTTCGACAATATCTATTACAATGTGATTAGAGTGATTAAGCTCATTATTGATGTAAAAAGTTTCAGACTTTAGCGAGGAATGGAAACTTTCTATCGGGGCGTTATCGGCAGGTGTTCCC  <  USA300TCH1516_ALE/68655‑68523

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.