New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 800928	27 (0.920)	3 (0.110)	3/246	NT	8.0%	intergenic (+62/‑289)	hisC_1/USA300HOU_RS03915	Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase
	?	USA300TCH1516_ALE	801948 =	43 (1.550)					intergenic (+189/+435)	USA300HOU_RS03915/USA300HOU_RS03920	Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase

AAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATCA  >  USA300TCH1516_ALE/801810‑802086                                                                                                                                           |                                                                                                                                           aaGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATa                                                                                                                                          >  2:286556/1‑141 (MQ=255)    tAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAg                                                                                                                                       >  2:111747/1‑141 (MQ=255)         gtgACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATa                                                                                                                                  <  1:159725/141‑1 (MQ=255)          tgattgatATGAACTTTTATGTCTTAGCCACTACAACACTATATTGTCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATAc                                                                                                                                 <  1:164157/141‑1 (MQ=255)           gACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGacaatct                                                                                                                                >  2:284628/1‑135 (MQ=255)                              aaaatgataaaatgttagaagttttatcaaactttaaatacgaatagtaagtggggagtgggacagaaatgatactttcgcaaaatttatttcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTa                                                                                                             >  2:340724‑M2/110‑141 (MQ=255)                               tCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAGATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTAt                                                                                                            <  1:205875/141‑1 (MQ=255)                               tCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTAt                                                                                                            <  1:205880/141‑1 (MQ=255)                                      cacTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTAt                                                                                                     >  2:115893/1‑141 (MQ=255)                                      cacTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTAt                                                                                                     <  1:273425/141‑1 (MQ=255)                                         tACAACACTATATTGCCAGTAGTTGACTGCGGTGCCCCAACATAGAGAAATTCGAACGCCAATTTCTACAGACAATTCAACTTGGTGTCTGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCa                                                                                                  <  2:234627/141‑1 (MQ=18)                                                  atatTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTaa                                                                                         >  1:123709/1‑141 (MQ=255)                                                  atatTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTaa                                                                                         >  2:217675/1‑141 (MQ=255)                                                       ggCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCAt                                                                                    >  1:300011/1‑141 (MQ=255)                                                          agtagtTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATGCTTTTTCTTTAGAAATTAGGATTTCTTATGCATGCGTGTAACTCATGCa                                                                                 >  1:327256/1‑141 (MQ=255)                                                          agtagtTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCa                                                                                 >  1:283911/1‑141 (MQ=255)                                                          agtagtTGACTGCGAGGCCCCAACATAGACAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCa                                                                                 >  1:191588/1‑141 (MQ=255)                                                              gtTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCa                                                                             >  2:237690/1‑141 (MQ=255)                                                                tGACTGGGGGGCTCCAACATAGAGGAATTTGAACGCTGTTGGCTACAGACCATGCGGGATGGGGGTGCCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTATTATGCATGAGTGTAACTCATGCATTCata                                                                           >  2:263350/1‑141 (MQ=17)                                                                tGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATCCTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACGCATGCATTCata                                                                           >  2:279727/1‑141 (MQ=255)                                                                          gCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTa                                                                 >  1:208292/1‑141 (MQ=255)                                                                               agtggggagtgggacagaaatgatactgtcgcaaaatttatgtcgtcgtcccaccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAt                                                            <  1:17605‑M2/81‑1 (MQ=255)                                                                               aaCATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAt                                                            >  1:39387/1‑141 (MQ=255)                                                                               aaCATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAt                                                            >  1:91432/1‑141 (MQ=255)                                                                               aaCATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAt                                                            >  2:332021/1‑141 (MQ=255)                                                                                aCATAGAGAAATTGGAACGCCAATTTGTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACAtt                                                           <  1:217675/141‑1 (MQ=255)                                                                                  aTAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATCCATTCATATTTTTAAGTACACATAAg                                                         >  1:305040/1‑141 (MQ=255)                                                                                    agagAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACGTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCt                                                       <  2:101540/141‑1 (MQ=255)                                                                                     gagaAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCCTGCATTCATTTTTTTAAGTACACATTAGCtg                                                      >  2:221318/1‑141 (MQ=255)                                                                                     gagaAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCtt                                                      >  2:153432/1‑140 (MQ=255)                                                                                      agaAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATAATTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTACCtgt                                                     >  1:320555/1‑141 (MQ=255)                                                                                        aaaTTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTTTTTTTTTTTTAGTATTTCTTATGCATTAGTGTAACTCATGCATTCATTTTTTTAAGTACATTTTAGCtttca                                                   >  2:75810/1‑137 (MQ=18)                                                                                        aaaTTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGa                                                   >  2:44277/1‑141 (MQ=255)                                                                                                aCGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGAt                                           >  1:153426/1‑141 (MQ=255)                                                                                                    cAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTCTGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACCCATTGACTGTGACTAATGCTaaaa                                       >  1:286460/1‑140 (MQ=18)                                                                                                      agtccTACAGACAATGCAAGGTGGGGTGGGCCGCAACAGAAAGAAATGCTTTTTCTTTAAAAATTAGTATTTAGTATGCAGGAGTGTAACTCATGCATTCATATTTGTAAGTACACATTAGCTGTGACTAATGATAAAGaa                                     <  2:142684/137‑1 (MQ=18)                                                                                                          cTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTTGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGc                                 <  2:193693/141‑1 (MQ=255)                                                                                                          cTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGc                                 <  2:275110/141‑1 (MQ=255)                                                                                                           tACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCGTTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGca                                >  2:217457/1‑140 (MQ=255)                                                                                                            aCAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTa                               >  1:205947/1‑141 (MQ=255)                                                                                                                aaatttatttcgtcgtccccccccaacATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATa                           <  1:326870‑M2/114‑1 (MQ=255)                                                                                                                   aTGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaata                        >  2:127010/1‑140 (MQ=255)                                                                                                                   aTGCAAGTTGGGGTGGGCCCCAACATAAAGAAATAATTTTACGCTATGAAATAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAAGCGCGACATaatc                        >  1:337559/1‑141 (MQ=18)                                                                                                                       aaGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATATCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATaatccatc                    >  1:240131/1‑141 (MQ=255)                                                                                                                         gTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATAAATCAt                  >  2:259098/1‑141 (MQ=255)                                                                                                                           tGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTa                <  1:111747/141‑1 (MQ=255)                                                                                                                            ggggTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAg               <  2:205947/141‑1 (MQ=255)                                                                                                                                         acATAAAGTAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTATACATTAGCCGTGACTAATGATAAAGAATCGCTACATAATAAATCATTACTCGTTCTTTAtcc  >  2:12793‑M2/3‑140 (MQ=255)                                                                                                                                           |                                                                                                                                           AAGTAATTGTGACTGAGATGAACTTTTATGTCTTAGACACTACAACACTATATTGGCAGTAGTTGACTGCGGGGCCCCAACATAGAGAAATTGGAACGCCAATTTCTACAGACAATGCAAGTTGGGGTGGGCCCCAACATAAAGAAATACTTTTTCTTTAGAAATTAGTATTTCTTATGCATGAGTGTAACTCATGCATTCATATTTTTAAGTACACATTAGCTGTGACTAATGATAAAGAATCGCTACATAATCAATCATTAGTCGTTCTTTATCA  >  USA300TCH1516_ALE/801810‑802086

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.