New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2872577	193 (1.060)	15 (0.090)	12/232	NT	7.5%	intergenic (‑113/+14)	rnpA/rpmH	Ribonuclease P protein component/50S ribosomal protein L34
	?	USA300TCH1516_ALE	= 2872581	193 (1.160)					intergenic (‑117/+10)	rnpA/rpmH	Ribonuclease P protein component/50S ribosomal protein L34

AAATCTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2872427‑2872577 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagatcactgaCTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCGAATTAA  <  USA300TCH1516_ALE/2872581‑2872442                                                                                                                                                                                                                                                                                                       AAATCTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAA                                                                                                                                                         >  1:1333255/1‑141  AATCTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAA                                                                                                                                                        >  2:198827/1‑141  AATCTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTACTGAGCTGATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAA                                                                                                                                                        <  2:155929/141‑1    TCTGCATTCTTTTTTATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGA                                                                                                                                                      <  3:567060/141‑1     CTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGAT                                                                                                                                                     >  1:1146389/1‑141     CTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGAT                                                                                                                                                     <  1:536816/141‑1     CTGCATTCTTTTTAATTCGGTAAGATATATACAAAAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTAAAAAAAAAAAAAAAAAAAGAT                                                                                                                                                     <  2:1143595/141‑1       GCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCA                                                                                                                                                   >  3:210983/1‑141        CATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATCACATAAATTTCTATTTATTCTTAATTTAAACGAAAAACAAGATCAC                                                                                                                                                  >  4:249238/1‑141        CATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATAACTCGCTCATTTATAG‑TTTTTATTGGAAGTGATGGTGAAACTTCTGTTGAGCTTGGAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCAC                                                                                                                                                  >  1:745280/1‑141         ATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACT                                                                                                                                                 >  2:670221/1‑141         ATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACT                                                                                                                                                 >  2:460888/1‑141         ATTCTTTATAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACT                                                                                                                                                 >  3:624862/1‑141          TTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTG                                                                                                                                                <  1:17662/141‑1          TTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTG                                                                                                                                                >  1:1624069/1‑141          TTCTTTTTAATTCGGTAAGCTTTTTCCAATAACAGCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTG                                                                                                                                                <  1:1535255/141‑1           TCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGA                                                                                                                                               <  2:1272752/141‑1           TCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGA                                                                                                                                               <  3:224572/141‑1                TTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑T                                                                                                                                         <  1:609398/141‑1                TTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑T                                                                                                                                         <  1:682819/141‑1                TTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑T                                                                                                                                         <  2:777132/141‑1                   ATTCTGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAG                                                                                                                                      <  1:1203273/141‑1                   ATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAG                                                                                                                                      <  1:440662/141‑1                      CGGTAAGCTTTTTCCAATCACATCTCTCGCTTATTTTTCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAGCGAAAAAAAAGATCGCTGTCTCA‑TCTGTGA                                                                                                                                   <  2:551570/141‑1                      CGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGTGA                                                                                                                                   <  1:932992/141‑1                       GGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGTGAT                                                                                                                                  <  1:161723/141‑1                        GTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCGTTTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGTGAT                                                                                                                                  <  1:1323677/141‑1                        GTAAGCTTTTTCCAAATACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGTGATC                                                                                                                                 <  1:207987/141‑1                         ttctcaTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGTGATCT                                                                                                                                <  2:1306814/135‑1                                                                           GCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGATGAG‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCA                                                                               >  1:663142/1‑141                                                                                                 GCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGATGAG‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTTTAAGCTCAATAGAAGTTTATATATAGCTTt                                                         >  2:1377776/1‑140                                                                                                      TAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGA‑TGAGTCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATA                                                    >  1:755557/1‑141                                                                                                                    ATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGT                                                                                                                                     >  1:1491915/1‑46                                                                                                                    ATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGACTCA‑TCAGT                                                                                                                                     <  2:1491915/46‑1                                                                                                                        ATTCTTAATTTAAACGAAAAAAAAGATCACTGA‑TGAGTCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTAAAATAAAAACGATAAATAAGCGA                                  >  1:1262269/1‑141                                                                                                                                       GAAAAAAAAGATCACTGATGAG‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAA                   >  4:347139/1‑141                                                                                                                                                GATCACTGACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTAC          <  4:68838/141‑1                                                                                                                                                 ATCACTGACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACC         <  2:408872/141‑1                                                                                                                                                  TCACTGACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCG        <  3:118632/141‑1                                                                                                                                                  TCACTGACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCG        >  2:1463439/1‑141                                                                                                                                                  TCACTCACTCA‑TCAGTGTTCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCG        <  3:276464/141‑1                                                                                                                                                    ACTGACTCA‑TCAGTGATCTTTTTTTTTGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCGAA      >  2:906808/1‑141                                                                                                                                                     CTGACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCTAGTGATGTTATTGGAAAAAGCTTACCGAAT     <  2:1488764/141‑1                                                                                                                                                      TGACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCGAATT    <  1:262930/141‑1                                                                                                                                                       GACTCA‑TCAGTGATCTTTTTTTTCTTTTATTTTAAGAATAAATAGAAATTTATGTTATAATCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTAATTGTAAAAAGCTTACCTAATTt   >  2:1120724/1‑140                                                                                                                                                       GACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAATAATAAATAGAAATTTATGTTATAAGCTCAATAAAAGATTAAATATAGCTTCAAATAAATACAATTAATAGGCGAGAGATTTTATCGTAAAAAGCATATCGAATTA   >  1:1307513/1‑141                                                                                                                                                       GACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCGAATTA   >  2:1567309/1‑141                                                                                                                                                        ACTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCGAATTAA  >  1:1174167/1‑141                                                                                                                                                                                                                                                                                                       AAATCTGCATTCTTTTTAATTCGGTAAGCTTTTTCCAATAACATCACTCGCTTATTTATCG‑TTTTTATTTGAAGCTATATTTAAACTTCTATTGAGCTTATAACATAAATTTCTATTTATTCTTAATTTAAACGAAAAAAAAGATCACTGA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2872427‑2872577 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aagatcactgaCTCA‑TCAGTGATCTTTTTTTTCGTTTAAATTAAGAATAAATAGAAATTTATGTTATAAGCTCAATAGAAGTTTAAATATAGCTTCAAATAAAAACGATAAATAAGCGAGTGATGTTATTGGAAAAAGCTTACCGAATTAA  <  USA300TCH1516_ALE/2872581‑2872442

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.