New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2085296 =	37 (0.910)	6 (0.170)	5/232	NT	17.4%	coding (173/201 nt)	hlb_1	Phospholipase C
	?	USA300TCH1516_ALE	= 2128343	24 (0.660)					coding (1/825 nt)	hlb_2	Phospholipase C

CGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAA  >  USA300TCH1516_ALE/2128211‑2128483                                                                                                                                     |                                                                                                                                             cGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTAAAAAATTTAGAGACAGAAAAAAAACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcca                                                                                                                                      <  1:214668‑M2/141‑9 (MQ=255)    ttaTTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaac                                                                                                                                   >  1:103339‑M2/2‑130 (MQ=255)     tATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaact                                                                                                                                  >  1:400276‑M2/1‑129 (MQ=255)       ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatcctacctgg                                                                                                                                <  1:375703‑M2/141‑15 (MQ=255)       ttCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactgg                                                                                                                                <  1:88837‑M2/141‑15 (MQ=255)         ctcATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggag                                                                                                                              >  1:374982‑M2/1‑125 (MQ=255)                  tAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAACCTAGGAGCAatatca                                                                                                                     >  2:160249/1‑139 (MQ=255)                   agaagaAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACACAATATTTACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATaaa                                                                                                                    >  1:414132/1‑141 (MQ=255)                    aaagaaAAAATAAATGAAGAGTAAAAAAAAACAACTAAATTTTTAGAAAGTATGTAATTTAGGGACCCATTATGGAATCCAGACACAATAAATACTGTTGTTACAAGGTTTCTATTTATCCAAACTGGGGGCAATATAAAc                                                                                                                   <  2:302245/140‑1 (MQ=255)                         aaaaTTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCt                                                                                                              <  2:71599/141‑1 (MQ=255)                                 aTGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACACGCCACACACGAAGATTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatc                                                                                                      <  1:364484‑M2/141‑41 (MQ=255)                                 aTGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGAACCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatc                                                                                                      >  2:157816‑M2/1‑101 (MQ=255)                                    aagaagAAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAAGACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                   <  2:168761/141‑1 (MQ=255)                                    aaGAGGACAAAAAAACAACTAAAATGTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCgg                                                                                                   <  1:351082/141‑1 (MQ=255)                                     agaagaAAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGa                                                                                                  <  2:171267/141‑1 (MQ=255)                                        ggACAAAAAAACAACTAAAATTTTAGACAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACaa                                                                                               <  1:435192/141‑1 (MQ=255)                                               aaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATcttctt                                                                                        >  1:452399/1‑141 (MQ=255)                                                   ccactaAAATTTTATAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacag                                                                                    >  2:341117‑M2/3‑83 (MQ=255)                                                    aacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGTGCAATATAAACGCGCTGATTTAATCAGACAAGCTGCTTAGAtt                                                                                   >  2:397873/1‑141 (MQ=255)                                                          aaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaat                                                                             <  2:163006/141‑1 (MQ=255)                                                          aaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAaat                                                                             <  1:281115/141‑1 (MQ=255)                                                                  aaaGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGt                                                                     >  1:132186/1‑141 (MQ=255)                                                                        tGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtaaccaaactggagacttttaacataaaattaaaaataaaaaaaaaagtaaaacagcataatatcaaggtttataac                                                               >  2:138937‑M2/1‑62 (MQ=255)                                                                            aTTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataacttta                                                           <  1:418154‑M2/141‑84 (MQ=255)                                                                            aTTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataacttta                                                           <  1:316332‑M2/141‑84 (MQ=255)                                                                               aaaggACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAAt                                                        <  2:478674/138‑1 (MQ=255)                                                                                      ccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCAt                                                 >  1:335475/1‑141 (MQ=255)                                                                                            gggACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGACGCATTTGATa                                           >  1:378230/1‑141 (MQ=255)                                                                                                ctacAAATCCAAGAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATgg                                       <  2:8292/138‑1 (MQ=255)                                                                                                cTCCAAACCCAATATATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATAGTCAATGAAGCATTTGATAATgg                                       <  2:70089/141‑1 (MQ=255)                                                                                                 tCCAAACCCAATAAATGCTGTTGTTACAAGGTTTCTATGTACCCGATTTGTGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGt                                      <  1:93194/141‑1 (MQ=255)                                                                                                 tCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGt                                      <  2:362599/141‑1 (MQ=255)                                                                                                     aaCCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCAt                                  >  1:398298/1‑141 (MQ=255)                                                                                                                    gttgttACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTaa                   >  1:406447/1‑141 (MQ=255)                                                                                                                        ttACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTaa               >  1:455700/1‑141 (MQ=255)                                                                                                                           cAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATATCGTAATATTAAATGAAGCATTTGATAATGGTGCATCACACAAATTATTACATAAtgt            >  2:145303/1‑141 (MQ=255)                                                                                                                                    tATGTATCCAAACTGGGGGCAATATAAAAGAGCTAATTTAATCGGAAAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGa   <  2:452399/141‑1 (MQ=255)                                                                                                                                     atgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttttaagttaatcattatcaataatacctcatataaaataaaattttagggccttattagggacttta  <  2:431604‑M2/141‑141 (MQ=255)                                                                                                                                     aTGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGaa  >  1:366175/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                                             CGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAAAGAA  >  USA300TCH1516_ALE/2128211‑2128483

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.