New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2681949 =	181 (0.990)	5 (0.030)	5/244	NT	2.8%	coding (873/1278 nt)	mvaA	3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase
	?	USA300TCH1516_ALE	2681984 =	170 (0.970)					coding (838/1278 nt)	mvaA	3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase
Rejected: Frequency below/above cutoff threshold.

ATGGAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2682092‑2681949 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTCG  >  USA300TCH1516_ALE/2681984‑2682123                                                                                                                                                                                                                                                                                              ATGGAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATAC                                                                                                                                                 <  2:528950/141‑1   GGAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGC                                                                                                                                               >  1:1523224/1‑141   GGAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGC                                                                                                                                               >  2:987791/1‑141   GGAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGC                                                                                                                                               >  2:389659/1‑141    GAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG                                                                                                                                              >  4:251035/1‑141    GAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG                                                                                                                                              >  2:1177951/1‑141    GAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG                                                                                                                                              <  2:1184886/141‑1    GAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG                                                                                                                                              >  2:1226094/1‑141    GAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG                                                                                                                                              <  2:711766/141‑1                                        CGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGC                                                                                                          <  3:386427/141‑1                                                                                                              CGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATATACTTGGGCCAATACAGAAGCACGTTC                                    >  4:132236/1‑141                                                                                                               GCGTGGTGCAGAAGCAAGTGCGCATGCATACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCC                                   >  1:419451/1‑141                                                                                                                  TGGTGCAGAAGCAAGTGCGCATGCATACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATT                                >  4:40930/1‑141                                                                                                                        AGAAGCAAGTGCGCATGCATACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTG                          >  4:403785/1‑141                                                                                                                                            ACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCT      >  2:154985/1‑141                                                                                                                                            ACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAA                      <  1:1362975/125‑1                                                                                                                                            ACGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAA                      >  2:1362975/1‑125                                                                                                                                             CGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTC     <  3:152366/141‑1                                                                                                                                             CGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTC     >  3:389855/1‑141                                                                                                                                             CGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTC     >  3:580977/1‑141                                                                                                                                             CGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTC     <  1:841494/141‑1                                                                                                                                             CGCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCACTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTC     <  1:944585/141‑1                                                                                                                                              GCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCT    <  1:467820/141‑1                                                                                                                                              GCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCT    <  1:1237750/141‑1                                                                                                                                              GCGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCT    <  4:560527/141‑1                                                                                                                                               CGTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTC   >  4:434072/1‑141                                                                                                                                                GTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTCG  <  1:489249/141‑1                                                                                                                                                                                                                                                                                              ATGGAACGTGCTTCTGTATTGGCCCAAGTAGATATTCATCGTGCAGCAACACATAATAAAGGTGTTATGAATGGCATACATGCTGTTGTTTTAGCAACAGGAAATGATACGCGTGGTGCAGAAGCAAGTGCGCATGCATACGCG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/2682092‑2681949 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑acgcgTATCATTTCCTGTTGCTAAAACAACAGCATGTATGCCATTCATAACACCTTTATTATGTGTTGCTGCACGATGAATATCTACTTGGGCCAATACAGAAGCACGTTCCATTCGTTTGGCAACCTCTTCTCCAGTTCTCTCG  >  USA300TCH1516_ALE/2681984‑2682123

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