New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	329202 =	129 (1.360)	7 (0.080)	6/246	10.1	5.9%	intergenic (+70/+73)	USA300HOU_RS01475/ssaA2_1	hypothetical protein/Staphylococcal secretory antigen ssaA2
	?	USA300TCH1516_ALE	329255 =	103 (1.180)					intergenic (+123/+20)	USA300HOU_RS01475/ssaA2_1	hypothetical protein/Staphylococcal secretory antigen ssaA2
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TGGATTGGTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/329349‑329202 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggtcgctttTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTTCATTTCTGAAATTAGAATACTTCCATCAATATTAACTTTT  >  USA300TCH1516_ALE/329255‑329392                                                                                                                                                                                                                                                                                                 TGGATTGGTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGG                                                                                                                                                    >  2:210049/1‑141  GGATTGGTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGT                                                                                                                                                   >  3:346031/1‑141  GGATTGGTGAATATAACGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCACAATTGGT                                                                                                                                                   >  3:346041/1‑141   GATTGGTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTC                                                                                                                                                  >  3:153415/1‑141       GGTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTT                                                                                                                                              <  1:175954/141‑1        GTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATACGTAACACTGCAAAATTGGTCGCTTT                                                                                                                                             >  1:371254/1‑141                                                                              TAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTTATTTTGTATGTTATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTT                                                                       >  2:137070/1‑141                                                                                    TGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATAGGTCTCTTTATTTTGTATGTCATGATTAATTTAATGGATGTAATTATATGATGAACCTTCTGAAGCAAAGATGGTTTTTGATGAA                                                                 >  2:167020/1‑141                                                                                                      ACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCACTCC                                              >  2:348002/1‑141                                                                                                          GTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTT                                          >  1:627562/1‑141                                                                                                          GTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTT                                          >  3:243947/1‑141                                                                                                              GCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACG                                                              <  2:146161/117‑1                                                                                                              GCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACG                                                              >  1:146161/1‑117                                                                                                                                             GTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTTCATTTCTGAAATTAGAATACTTCCATCAATATTAA       >  3:191048/1‑141                                                                                                                                             GTCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTTCATTTCTGAAATTAGAATACTTCCATCAATATTAA       >  3:333815/1‑141                                                                                                                                              TCGCTTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTTCATTTCTGAAATTAGAATACTTCCATCAATATTAAC      <  4:6906/141‑1                                                                                                                                                  TTTTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATAGACGCCAATCCAGTTCATTTCTGAAATTAGAATACTTCCATCAATATTAACTTTT  >  1:450444/1‑141                                                                                                                                                                                                                                                                                                 TGGATTGGTGAATATATCGTTTCATCAAGAACCATCTCTGCTTCAGAAGTTTCATCATATAATTACATCCATTAAATTAATCATGACATCAATAAAAAGCGACCAGTTCGCAGTTTACAATTCGTAACACTGCAAAATTGGTCGCTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/329349‑329202 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tggtcgctttTTATTG‑ATGTCATGATTAATTTAATGGATGTAATTATATGATGAAACTTCTGAAGCAGAGATGGTTCTTGATGAAACGATATATTCACCAATCCAGTTCATTTCTGAAATTAGAATACTTCCATCAATATTAACTTTT  >  USA300TCH1516_ALE/329255‑329392

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.