New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1822865 =	129 (1.040)	7 (0.060)	7/240	NT	5.7%	intergenic (+186/+60)	USA300HOU_RS09070/ackA	Putative universal stress protein/Acetate kinase
	?	USA300TCH1516_ALE	1822909 =	110 (0.950)					intergenic (+230/+16)	USA300HOU_RS09070/ackA	Putative universal stress protein/Acetate kinase

CTCATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1823013‑1822865 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tagacgcttAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTAGTAAG  >  USA300TCH1516_ALE/1822909‑1823048                                                                                                                                                                                                                                                                                                       CTCATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGT                                                                                                                                                       <  2:165582/141‑1  TCATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTA                                                                                                                                                      <  2:526488/141‑1  TCATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGCTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTA                                                                                                                                                      <  2:573226/141‑1   CATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTGAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAG                                                                                                                                                     <  1:785033/141‑1   CATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAG                                                                                                                                                     <  1:53991/141‑1   CATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAG                                                                                                                                                     <  1:54178/141‑1   CATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAG                                                                                                                                                     >  2:128317/1‑141    atcCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGA                                                                                                                                                    <  1:1048031/138‑1    ATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGA                                                                                                                                                    >  1:1017090/1‑141    ATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGA                                                                                                                                                    >  1:957973/1‑141    ATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGA                                                                                                                                                    >  1:941942/1‑141     TTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGAC                                                                                                                                                   >  1:750456/1‑141      TCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACG                                                                                                                                                  >  1:696123/1‑141        ACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCT                                                                                                                                                <  2:972372/141‑1        ACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCT                                                                                                                                                <  1:633256/141‑1                     GTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTACCTC‑‑CTACATATAAT‑TGTAGCGGAGATAGACGCTTAATAT‑TTATTTA                                                                                                                                  <  2:374254/141‑1                              CCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTACCTC‑‑CTACATATAAT‑TGTAGCGGAGATAGACGCTTAATAT‑TTATTTAAAAATTATT                                                                                                                         <  3:280309/141‑1                                                       CCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCAACTACA‑ATTATATGTA‑‑GTATGTATACGCTTAATAT‑TTATTTAAAAATTATTTTAAACAACCAAATGTAATAACATC                                                                                                >  2:900948/1‑141                                                                                                              GTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTAAACTGGTGAA                                         >  3:222707/1‑141                                                                                                                 TATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTAGAATAACGACAACTTTAACTGGTGAATGA                                      >  2:777578/1‑141                                                                                                                      CCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATA                                 >  1:151699/1‑141                                                                                                                       CGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCTTTTTGTATTGTTTGAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATA                                 >  2:137449/1‑141                                                                                                                                                  GACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGT        >  1:1042128/1‑141                                                                                                                                                  GACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGT        <  1:550169/141‑1                                                                                                                                                  GACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGT        >  1:545372/1‑141                                                                                                                                                   ACGCTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTA       >  3:337471/1‑141                                                                                                                                                      CTTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTAGTA    >  2:637287/1‑141                                                                                                                                                       TTAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTAGTAA   >  4:230595/1‑141                                                                                                                                                        TAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTAGTAAG  >  1:943766/1‑141                                                                                                                                                        TAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTAGTAAG  <  4:275200/141‑1                                                                                                                                                                                                                                                                                                       CTCATTCACCAGTTAAAGTTGTCGTTATTCCAACAGATGAAGAAAGTATGATTGCCCGTGATGTTATGACATTCGGTGGTTTAAAATAATTTTTAAATAAATATTAAGCGTCTATCTCCGCTACA‑ATTATATGTA‑‑GGAGGTAGACGCTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1823013‑1822865 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑tagacgcttAATAT‑TTATTTAAAAATTATTTTAAACCACCGAATGTCATAACATCACGGGCAATCATACTTTCTTCATCTGTTGGAATAACGACAACTTTAACTGGTGAATGAGGATAGTTAATAAATCCTTCTTTACCACGTAGTAAG  >  USA300TCH1516_ALE/1822909‑1823048

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.