New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2085296 =	15 (0.810)	9 (0.550)	9/240	0.7	37.2%	coding (173/201 nt)	hlb_1	Phospholipase C
	?	USA300TCH1516_ALE	= 2128343	17 (1.030)					coding (1/825 nt)	hlb_2	Phospholipase C

CGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAA  >  USA300TCH1516_ALE/2128211‑2128477                                                                                                                                      |                                                                                                                                       cGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtg                                                                                                                                      <  1:32896‑M2/135‑3 (MQ=255)      aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcc                                                                                                                                 >  2:173007‑M2/1‑128 (MQ=255)      aTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcc                                                                                                                                 <  1:145983‑M2/135‑8 (MQ=255)       ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAAAAACTAAAAATTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcca                                                                                                                                <  1:15939‑M2/135‑9 (MQ=255)         ctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACTCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaa                                                                                                                              >  1:134118‑M2/1‑125 (MQ=255)           cATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaact                                                                                                                            <  2:146410‑M2/135‑13 (MQ=255)           cATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACACATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAagtatccaagtt                                                                                                                            <  2:141945‑M2/135‑13 (MQ=255)             tttGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGTGT‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgg                                                                                                                          >  1:210412‑M2/1‑121 (MQ=255)             tgtgtTAGAAGAGAAATGTAATGAAGAAGAGAAAAAGACACCTATAGTTTTAGAAAGTATGTAATTTAGGGACCCATTATGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgg                                                                                                                          >  2:185382‑M2/3‑121 (MQ=255)                gTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGCA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggaga                                                                                                                       >  2:145592‑M2/1‑118 (MQ=255)                   agaagaAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTTCAAACCCTATAAATATTGTTGTTATAAGGTTTCTATGTATCCAAACTGGGGGCaa                                                                                                                    <  1:195081/135‑1 (MQ=255)                   agaagaAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAATCCAATTAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCaa                                                                                                                    <  1:22989/135‑1 (MQ=255)                     aagaaAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATTTATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagactttt                                                                                                                  >  1:187217‑M2/1‑113 (MQ=255)                              ttAATGAAGAGGACAAAAAAACCAATAGAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACgcgc                                                                                                         <  2:32896/135‑1 (MQ=255)                                 aTGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTTCAATCTCTATTATTTCTGTTGTTATAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGa                                                                                                      <  1:48071/135‑1 (MQ=255)                                  tGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATCTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAt                                                                                                     <  2:218800/135‑1 (MQ=255)                                   gAAGAGGACAAAACAACAACTAAAATTTTAGAAAATATATAATTTAGAGACCCATTAGAAA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGACAATATAAACGCACTGAtt                                                                                                    >  1:77174/1‑135 (MQ=255)                                    aaGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATATTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAttt                                                                                                   <  1:39015/135‑1 (MQ=255)                                       agGACAAAAAAACCACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCAAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAAt                                                                                                <  2:118756/135‑1 (MQ=255)                                         gACAAGAACATAACTAAAATTTTAGAAAGTATGTAATTTAGGGA‑ACACTACAGACCGTTCAATTGAATAACTACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGCGCAATATCAACGCGCTGATTTAATCg                                                                                              <  2:220171/135‑1 (MQ=255)                                         aaCAAATAAACTATTACAATTTTTGAAAGTATGTAATTTAGGGCCCTATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGTGGCAATATAAACGCTCTGATTTAAGCg                                                                                              <  2:186808/134‑1 (MQ=255)                                            aaaaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAAGGA‑ATAAAAAACAAATAAATAATATTGTTACAAGGTTTCTATGTATCCAAACTGGTGGCAATATAAACGCGCTGATTTAATCGGAc                                                                                           >  1:50007/1‑135 (MQ=255)                                                  acaacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagt                                                                                     >  2:145983‑M2/1‑84 (MQ=255)                                                       tAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaac                                                                                >  1:177722‑M2/1‑79 (MQ=255)                                                            ttttAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTaa                                                                           <  2:205071/135‑1 (MQ=255)                                                                                         ttAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGATTTCTATATATACAAAATGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAg                                              >  1:97232/1‑135 (MQ=255)                                                                                              gA‑CTCCAAACCCAATAAATAATGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaata                                         <  2:102036‑M2/135‑96 (MQ=255)                                                                                                  tCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaattaaaacagcataatatcaaggtttatacctttatcattatcaataata                                      <  2:68409‑M2/135‑99 (MQ=255)                                                                                                              aaataCTGTTGTTACAAGTTTCCTAtgtagccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaa                          >  1:79003‑M2/1‑25 (MQ=255)                                                                                                                  aCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACa                      >  2:183851/1‑135 (MQ=255)                                                                                                                    cgttgttaCAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaat                    >  2:185475‑M2/2‑19 (MQ=255)                                                                                                                                  ttCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGCTGTCGTAATATTCAATGAAGCATTTGATAATAGTGTATCAGACAAATTATTAATTAAtgt      >  2:105488/1‑135 (MQ=255)                                                                                                                                    cTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATAGAACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGAAAAATTATTAAGTAATGTGa    >  1:89591/1‑135 (MQ=255)                                                                                                                                     tAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaattttagggactttttagg   <  1:124459‑M2/135‑134 (MQ=255)                                                                                                                                      aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaa  <  1:183851/135‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       CGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGA‑CTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAA  >  USA300TCH1516_ALE/2128211‑2128477

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.