New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	979658 =	112 (1.140)	9 (0.100)	4/144	NT	8.5%	coding (601/870 nt)	ampR	HTH‑type transcriptional activator AmpR
	?	USA300TCH1516_ALE	979694 =	94 (1.060)					coding (565/870 nt)	ampR	HTH‑type transcriptional activator AmpR

TCCCAATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/979755‑979658 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcacttaTTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCAT  >  USA300TCH1516_ALE/979694‑979782                                                                                                                                                                                             TCCCAATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCA                                                                                                  >  1:3519248/1‑91  CCCAATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCAT                                                                                                 <  1:604802/91‑1    CAATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCA                                                                                               <  1:1218521/91‑1     AATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCAC                                                                                              <  1:1626231/91‑1     AATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCAC                                                                                              <  1:3555055/91‑1      ATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCACT                                                                                             >  1:2267715/1‑91        AAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTA                                                                                           >  1:1370926/1‑91        AAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTA                                                                                           >  1:3440653/1‑91                                                     TACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGAT                                              >  1:2346447/1‑91                                                         AAATAATAAGTGATAACCATCCAGAATATTGGTCATCTCTTATTATCTTGTATTTTTCACATAAAGATGCCTCAGTTAGAAGATGATTATT                                          >  1:3307001/1‑91                                                         AAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATT                                          >  1:627025/1‑91                                                         AAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATT                                          >  1:2584646/1‑91                                                         AAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATT                                          >  1:1039967/1‑91                                                              ATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTT                                     >  1:64329/1‑91                                                              ATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTT                                     >  1:64343/1‑91                                                              ATAAGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTT                                     >  1:1514362/1‑91                                                                 AGTGATAACCATCCAGAATATTGGTCATCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTAT                                  >  1:2415823/1‑91                                                                                            TCACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTT       >  1:792522/1‑91                                                                                             CACTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTC      >  1:2413066/1‑91                                                                                               CTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGC    <  1:2946652/91‑1                                                                                               CTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGC    <  1:2946328/91‑1                                                                                               CTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGC    <  1:2626405/91‑1                                                                                               CTTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGC    <  1:232974/91‑1                                                                                                TTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCA   >  1:2791593/1‑91                                                                                                TTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCA   <  1:276028/91‑1                                                                                                TTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCA   <  1:3796927/91‑1                                                                                                TTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCA   <  1:2285411/91‑1                                                                                                TTATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCA   <  1:1614943/91‑1                                                                                                 TATTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCAT  <  1:698781/91‑1                                                                                                                                                                                             TCCCAATAAAGAGAATAATCATCTTCTAACTGAGGCATCTTTATTTGAAAAATACAAAATAATAAGTGATAACCATCCAGAATATTGGTCATCACTTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/979755‑979658 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑atcacttaTTATTTTGTATTTTTCAAATAAAGATGCCTCAGTTAGAAGATGATTATTCTCTTTATTGGGAGCAATCAATACAATTTTACCTTCGCAT  >  USA300TCH1516_ALE/979694‑979782

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ 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.