Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	62,817	+TCAATT	100%	intergenic (‑284/+229)	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)	33 (1.000) +TCAATT	26/246	NT	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

AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/62681‑62817 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCC  >  USA300TCH1516_ALE/62818‑62952                                                                                                                                          ||||||                                                                                                                                        AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTTTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAA                                                                                                                                           <  2:262206/141‑1 AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAA                                                                                                                                           >  1:269276/1‑141        TTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTT                                                                                                                                    <  1:347014/141‑1          ATTAAAACAAAGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTT                                                                                                                                  <  2:10138/141‑1            TAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGACCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCATTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGT                                                                                                                                <  1:30380/141‑1            TAAAACAAAACAAACAATTCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGACCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGT                                                                                                                                <  1:12067/141‑1                 CAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAAGTTATTTTTGTTGAAA                                                                                                                           >  2:232504/1‑141                 CAACGAAAACAAGTCTTACTACAAAAATTGGTTGTTGAATTGTGATAACGTTCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAA                                                                                                                           <  2:173269/141‑1                             GGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCT                                                                                                               <  1:192200/141‑1                               CTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTC                                                                                                             <  1:135960/141‑1                                TTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTCAAATTAATATAAGCTTCA                                                                                                            >  2:114148/1‑141                                        AAAAATGTTTGTGTAATTCTGATAACGTCTTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATTCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATA                                                                                                    <  2:424781/141‑1                                            ATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTACAATCTGATAGATA                                                                                                >  2:104438/1‑141                                            ATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTGTTGTTGAAATTAATATAAGCTTCATTCTGATAGATA                                                                                                >  2:3145/1‑141                                                TTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCA                                                                                            <  1:286043/141‑1                                                   TGTAATTCTGATAACGTACTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGATCATCCCTTACAGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTA                                                                                         <  2:382551/141‑1                                                     TAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAAT                                                                                       <  1:226228/141‑1                                                                    CCTATTATGTTTATTGAGAATAGAGAAAAATAAATTGAGAGCATCCCGTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGGCATTAATATAAGCGTCATTGTGATAGATAGTCATTAATAATTGGTTGTAAATC                                                                        <  2:357449/141‑1                                                                     CTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTGATTAATAATTGTTTGCACATCG                                                                       >  2:130792/1‑141                                                                           TGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTCTTA                                                                 >  2:37639/1‑141                                                                           TGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTA                                                                 >  2:350667/1‑141                                                                            GTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAA                                                                >  2:168946/1‑141                                                                             TTAATTGAAAATAGACAAAAATAAATTGAGGGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAG                                                               <  2:238379/141‑1                                                                               AATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTAACTAATGGTTATTCAGTA                                                             >  2:232670/1‑141                                                                                             AAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCG                                               <  1:6010/141‑1                                                                                             AAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTAAATTTATTTTTGTTGAAATTAATAGAAGCTTCAGTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCG                                               <  1:5759/141‑1                                                                                                         AGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATA                                   <  1:253885/141‑1                                                                                                                   TTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGT                         >  2:429298/1‑141                                                                                                                   TTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGT                         <  1:322584/141‑1                                                                                                                    TACCGCAAAGTGAAGGATGCTCTAAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTA                        <  1:429487/141‑1                                                                                                                           AAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTAATGGATAGCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTA                 >  2:304819/1‑141                                                                                                                               GAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAA             >  1:236449/1‑141                                                                                                                                   GATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAAT         <  1:94640/141‑1                                                                                                                                   GATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAAT         <  1:66694/141‑1                                                                                                                                   GATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAAT         <  1:289311/141‑1                                                                                                                                     TGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTT       <  1:226944/141‑1                                                                                                                                          TCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCC  <  1:339300/141‑1                                                                                                                                          ||||||                                                                                                                                        AATAGAATTATTAAAACAACGCAAACAAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/62681‑62817 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCAAGAATTTATTCC  >  USA300TCH1516_ALE/62818‑62952

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.