New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	2085296 =	20 (0.810)	10 (0.450)	8/252	1.4	32.8%	coding (173/201 nt)	hlb_1	Phospholipase C
	?	USA300TCH1516_ALE	= 2128343	23 (1.030)					coding (1/825 nt)	hlb_2	Phospholipase C

CATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAA  >  USA300TCH1516_ALE/2128207‑2128479                                                                                                                                         |                                                                                                                                         cATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACCAAGATTTTAGAAAGTATGTAATTTAGGGACACATTAGGGACTCCAAACCCAATAAATAATGTTGTTACAAGGTTTCTCtgta                                                                                                                                      <  2:48200‑M2/141‑5 (MQ=255)   tCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatc                                                                                                                                    >  1:227373‑M2/1‑135 (MQ=255)      gtgtATTCTTATTTTTTAGAAGAAAAATTTAATGAAGAGAACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaa                                                                                                                                 >  1:160899‑M2/1‑132 (MQ=255)       tgtATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGAGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaa                                                                                                                                <  2:110577‑M2/141‑11 (MQ=255)                 tttGTTAGAAGAAAAATTTAAGGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCaa                                                                                                                      <  2:11976/141‑1 (MQ=255)                   tGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagactttt                                                                                                                    >  1:239447‑M2/1‑119 (MQ=255)                    gTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAatat                                                                                                                   >  1:274416/1‑141 (MQ=255)                                 tttAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagccttttaacataaaattact                                                                                                      <  2:126745‑M2/141‑37 (MQ=255)                                 attAATGAAGAGGACAAAAAAAAAACTAAAATTTTAGAAAGTATGTAATTTAAGGACCCATTAGGGACTCCAAACCCAATAAGTACTTTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGAtt                                                                                                      <  2:226474/140‑1 (MQ=255)                                                aaaaaaaCAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagactttcaacataaaattacttatccttcaaaaagt                                                                                       <  2:239909‑M2/141‑52 (MQ=255)                                                    aaaCAAATAAAATATTAGAAAGTATGTAATTTAGGGAGCCATTAGGGACTGCAAACGCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaa                                                                                   >  2:13762‑M2/1‑86 (MQ=255)                                                       caacTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTACTCGGACAATCTTCTTctat                                                                                >  2:220084/1‑141 (MQ=255)                                                         acTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAGTCTTGGTATATTa                                                                              >  1:37871/1‑141 (MQ=255)                                                           tAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcata                                                                            >  1:112411‑M2/1‑79 (MQ=255)                                                           tAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcata                                                                            >  1:83368‑M2/1‑79 (MQ=255)                                                           tAAAATTGTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcata                                                                            >  1:85226‑M2/1‑79 (MQ=255)                                                             aaaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTaaaaa                                                                          >  1:171350/1‑141 (MQ=255)                                                             aaaTTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAAAATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTaaaaa                                                                          >  1:234960/1‑141 (MQ=255)                                                                            tGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataac                                                           >  2:224359‑M2/1‑62 (MQ=255)                                                                              tAATTTAGGGACCCATTAGGGACTCCAAACCCAGTAAATACTGTTGTTACAAGGTTTCTAGGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAatat                                                         >  2:81278/1‑141 (MQ=255)                                                                              tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAatat                                                         >  2:28985/1‑141 (MQ=255)                                                                              tAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATAATGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAAAGCCACAACATAACCGGACAATCTTCTTATATTAAAAATAATGATGTAGTTatct                                                         >  2:277014/1‑139 (MQ=255)                                                                               aaTTTAGGGACCCATTAGGGAATCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATAtt                                                        >  1:249494/1‑141 (MQ=255)                                                                               aaTTTAGGGAACCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTCtgtatcccacctggagacttttaacataaaattaattatcatgccatctgtcaaactgcctaacatcaaggtttataacttt                                                        >  2:265714‑M2/1‑59 (MQ=255)                                                                                        aCCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGc                                               >  1:68765/1‑141 (MQ=255)                                                                                         cccATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCa                                              >  2:266036/1‑141 (MQ=255)                                                                                         cccATTAGAGACTCCAAACCCAATAAATACTGTTGTTACAAGGTATCTATGTATCCAAACTGGCGTAATTATAAAGACGCTGATTTAATCAAACAATCTTCTTATATTAAAAATAATGATGACGTAATATTCAATGAATCa                                              >  2:2876/1‑141 (MQ=255)                                                                                            aTTAGTGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCAttt                                           <  1:110577/141‑1 (MQ=255)                                                                                                    cTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGACGCATTTAATAATgg                                   >  2:270758/1‑141 (MQ=255)                                                                                                     tCCAAACCCAATAAATACTGTTGTCACCAGGGGTGTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGt                                  <  2:70917/141‑1 (MQ=255)                                                                                                                   ataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGTTGCATCAGACAAatt                    >  2:56413/1‑141 (MQ=255)                                                                                                                   ataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAatt                    >  1:174837/1‑141 (MQ=255)                                                                                                                   ataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAatt                    >  1:46118/1‑141 (MQ=255)                                                                                                                   ataCTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAAGATTCAATGAAGCATTTGATAATGGTGCATCAGACAAgtt                    >  2:50450/1‑141 (MQ=255)                                                                                                                                    tttGTATGTATGCAAAGTGGGTGCAATATAAACGCGCTGATTTAATCGGACAATCTTGTTATATTAAAAATAATGATGTCGTAATATTCAAGGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaga   <  2:281713/141‑3 (MQ=255)                                                                                                                                    tttCGATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGaaaa   <  2:200691/141‑1 (MQ=255)                                                                                                                                     ttCTAtgtatccaaactggagacttttaacataaaattacttatcattcaaaaagtaaaacagcataatatcaaggtttataactttatcattatcaataatacctcatataaaataaaatttgagggactttttagggac  <  1:79361‑M2/141‑137 (MQ=255)                                                                                                                                         |                                                                                                                                         CATCCGTGTATTCTCATTTGTTAGAAGAAAAATTTAATGAAGAGGACAAAAAAACAACTAAAATTTTAGAAAGTATGTAATTTAGGGACCCATTAGGGACTCCAAACCCAATAAATACTGTTGTTACAAGGTTTCTATGTATCCAAACTGGGGGCAATATAAACGCGCTGATTTAATCGGACAATCTTCTTATATTAAAAATAATGATGTCGTAATATTCAATGAAGCATTTGATAATGGTGCATCAGACAAATTATTAAGTAATGTGAAAAA  >  USA300TCH1516_ALE/2128207‑2128479

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.