New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	512620 =	15 (0.730)	23 (1.560) +TTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAA	19/200	0.0	68.3%	intergenic (+688/‑6075)	recR/speA_2	Recombination protein RecR/Arginine decarboxylase
	?	USA300TCH1516_ALE	1998278 =	NA (NA)					intergenic (‑6/+3329)	USA300TCH1516_01882/USA300TCH1516_01883	tRNA‑Val/tRNA‑Ala

CTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/512756‑512620 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATT  >  USA300TCH1516_ALE/1998278‑1998413                                                                                                                                          ||||||||||||||||||||||||||||||||||||||||                                                                                                                                         CTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTct                                                                                                                                                                              >  1:194664/1‑139   AAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCT                                                                                                                                                                            >  1:134848/1‑141       AATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTC                                                                                                                                                                        >  1:192821/1‑141                          TACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTCACCGACAAGAATTAATTATACATTTTATCAACATTTAACTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAA                                                                                                                                                     >  2:40688/1‑141                                ttttatAATTAACCTTCACATATTATCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAATAATTAATTATACATTTTATCAATATTTAAATCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTG                                                                                                                                               <  2:81672/135‑1                                TTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTAGACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTG                                                                                                                                               <  1:170450/141‑1                                  TTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGAT                                                                                                                                             >  1:85169/1‑141                                  TTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGAT                                                                                                                                             >  2:203225/1‑141                                  TTGGAATTAACGTTGACATATTGTCAGTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACCTTTTATCAACATTTAAGTCAATAACTTTTTTTAGCGTGTCCATTTTTTTTTTTATCCAAATTTTTAT                                                                                                                                             >  2:133300/1‑141                                       ATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTCAGTCAACAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAA                                                                                                                                        <  1:34931/141‑1                                                GACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTG                                                                                                                               <  1:137921/141‑1                                                  aATATTGTAATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTTAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGC                                                                                                                             <  2:121909/140‑1                                                  CATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGC                                                                                                                             <  2:187534/141‑1                                                   ATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGCCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCCACATTTGATTAAAAAACTGCCTCGCA                                                                                                                            >  1:205995/1‑141                                                      TTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACG                                                                                                                         >  1:91379/1‑141                                                         TCATTCATTTTTCAATGTTCATTTTTTTTATTAACAAGAATTAATTATATATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTC                                                                                                                      <  2:49603/141‑1                                                         TCATTCAGATTTTTATGTTCATTTCTCATACCCACAAGAAGTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTC                                                                                                                      <  1:65577/141‑1                                                                 TTTTCAATGTTCATTTTTATTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACTAAAATTTGATTAAAAAATTAACTTTTAACTTTCTACTCTAt                                                                                                              >  2:119358/1‑140                                                                        TGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACG                                                                                                       <  2:43300/141‑1                                                                           TCATTTTTCTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAA                                                                                                    <  2:192821/141‑1                                                                                   CTTACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACT                                                                                            >  1:148181/1‑141                                                                                     TACCGACAAGAATTAATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTAC                                                                                          <  2:89815/141‑1                                                                                                   AATTATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAATCTAAATTTGCTTAAAAAACTGCCTGGTAACGTTATACTCTAGCGGAACGTAAGTTTGTCTACACTCGACGCTAAct                                                                            >  2:166851/1‑139                                                                                                      TATCCATTTTATCAACATTTAAGTCAGTAACTTTTCTTATCGTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTGCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGC                                                                         <  1:81984/141‑1                                                                                                      TATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGC                                                                         <  1:42557/141‑1                                                                                                      TATACATTTTATCAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGC                                                                         <  1:231001/141‑1                                                                                                           tTTTTATGAACATTTAATTCAATAACTTTTTTTATCTGGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAAC                                                                    <  2:71823/140‑1                                                                                                            TTTTAGTAATATTTAAGTCTATAACTTTTTTTATCTTGCACATTTTATTATTTAACCAGAATTTGAGTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGCAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACT                                                                   <  2:205852/141‑1                                                                                                             TTTATCAACATGTAAGGCAATAACGTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGAACACGTTCTAGGCGAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTT                                                                  <  1:34691/141‑1                                                                                                                 tcAACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGT                                                              <  1:13671/139‑1                                                                                                                    ACATTTAAGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTT                                                           >  1:128246/1‑141                                                                                                                           AGTCAATAACTTTTTTTATCTTGTCCATTTTATTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATG                                                    <  1:171163/141‑1                                                                                                                                                           TTTTTTAACCAAAATTTGATTAAAAAACTGCCTGGCAACATTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACTCTAAGGAGCTTAACGTCTGTGTTCGGCATGGGCACAGGTCTCACCTCCTTTCATTAGTCACC                    >  2:132329/1‑141                                                                                                                                                                             ATTAAAAAACTGGCTGGAAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAtaa  <  1:4628/141‑4                                                                                                                                                                             ATTAAAAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATT  >  1:170087/1‑141                                                                                                                                          ||||||||||||||||||||||||||||||||||||||||                                                                                                                                         CTAAATAATGTTTGTAACTTATAGTTACGTTTTTTGGAATTAACGTTGACATATTGTCATTCAGTTTTCAATGTTCATTTTTCTTACCGACAAGAATTAATTATACATTTTATTAACATTTAAGTCAATAACTTTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/512756‑512620 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑AAAACTGCCTGGCAACGTTCTACTCTAGCGGAACGTAAGTTCGACTACCATCGACGCTAAGGAGCTTAACTTCTGTGTTCGGCATGGGAACAGGTGTGACCTCCTTGCTATAGTCACCAGACATATGAATGTAATT  >  USA300TCH1516_ALE/1998278‑1998413

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.