New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2681949 =	134 (0.660)	10 (0.050)	7/150	NT	7.0%	coding (873/1278 nt)	mvaA	3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase
	?	USA300TCH1516_ALE	2681984 =	142 (0.740)					coding (838/1278 nt)	mvaA	3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase

CATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2682041‑2681949 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCA  >  USA300TCH1516_ALE/2681984‑2682073                                                                                                                                                                                          CATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACG                                                                                              >  1:1266989/1‑91  ATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACGC                                                                                             >  2:3241536/1‑91                                                       GATACGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACGCGAGTCATTTCCTGTTGCTAAAACAACAGCATGTACGCCATTCATAACACCTTT                                        >  2:3714966/1‑91                                                           CGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTA                                    >  1:2324730/1‑91                                                           CGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTA                                    >  1:3606839/1‑91                                                               TGGTGCAGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTG                                >  1:2809854/1‑91                                                                GGTGCAGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGT                               >  1:2336302/1‑91                                                                GGTGCAGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGT                               >  1:2673328/1‑91                                                                  TGCAGAAGCAAGTGCGCATGCACCACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACCCCTTCATTATGCGTT                              >  2:3798008/1‑91                                                                   GCAGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATGATGTGCTGC                            >  1:3552413/1‑91                                                                     AGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTG                          >  2:708288/1‑91                                                                     AGAAGCAAGTGCGCATGCA‑TACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTG                          >  2:2496480/1‑91                                                                                          ACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGG      <  1:1855348/91‑1                                                                                          ACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGG      >  2:2952186/1‑91                                                                                          ACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGG      <  1:1855384/91‑1                                                                                           CGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGG     >  1:2523600/1‑91                                                                                           CGCGTATCATGTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGG     <  2:1473518/91‑1                                                                                            GCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGC    <  1:3934323/91‑1                                                                                            GCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGC    >  2:3722840/1‑91                                                                                             CGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCC   <  1:3714511/91‑1                                                                                              GTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCA  >  2:2062539/1‑91                                                                                                                                                                                          CATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCA‑TACGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2682041‑2681949 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCA  >  USA300TCH1516_ALE/2681984‑2682073

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.