New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2751374	159 (0.830)	24 (0.140)	12/146	NT	13.9%	intergenic (‑222/+39)	betA/gbsA	Oxygen‑dependent choline dehydrogenase/Betaine aldehyde dehydrogenase
	?	USA300TCH1516_ALE	= 2751393	153 (0.880)					intergenic (‑241/+20)	betA/gbsA	Oxygen‑dependent choline dehydrogenase/Betaine aldehyde dehydrogenase

ATTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2751278‑2751374 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtgagtgCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATAG  <  USA300TCH1516_ALE/2751393‑2751304                                                                                                                                                                                             ATTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTGTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAG                                                                                                  <  2:3473920/91‑1  TTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGT                                                                                                 <  2:2567846/91‑1  TTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGT                                                                                                 <  2:1290277/91‑1  TTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGT                                                                                                 <  2:1110432/91‑1  TTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGT                                                                                                 >  1:2093803/1‑91   TGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTG                                                                                                >  2:2932229/1‑91      TACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGT                                                                                             >  1:3875754/1‑91       ACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTG                                                                                            <  1:2264035/91‑1       ACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTG                                                                                            >  1:1560127/1‑91       ACTAACAGGAATGAAATAATCTATGAGTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTG                                                                                            <  1:2523967/91‑1                       TAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACA                                                                            <  1:655206/91‑1                         ATCTATGATTCATTTTGCGTTTAGTCCAAGTTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAG                                                                          <  1:3105746/91‑1                          TCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGA                                                                         <  2:2135183/91‑1                          TCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGA                                                                         <  2:1916996/91‑1                          TCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGA                                                                         <  1:333743/91‑1                           CTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGAC                                                                        <  1:1043045/91‑1                           CTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGAC                                                                        <  2:2129766/91‑1                           CTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGAC                                                                        <  2:1410566/91‑1                           CTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGAC                                                                        <  1:2511292/91‑1                           CTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGAC                                                                        <  1:3283628/91‑1                            TATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACA                                                                       <  1:3591161/91‑1                            TATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACA                                                                       <  1:1351535/91‑1                             ATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACAC                                                                      <  1:2218387/91‑1                              TGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACT                                                                     <  1:2456541/91‑1                               GATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTC                                                                    <  1:3639922/91‑1                               GATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTC                                                                    <  2:156297/91‑1                                ATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCA                                                                   <  2:1388331/91‑1                                ATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCA                                                                   <  2:1147753/91‑1                                ATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCA                                                                   <  2:1147543/91‑1                                ATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCA                                                                   <  2:419212/91‑1                                ATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCA                                                                   <  2:419303/91‑1                                 TTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCAC                                                                  <  2:3446896/91‑1                                 TTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAG                                                                                              <  2:766007/63‑1                                 TTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAG                                                                                              >  1:766007/1‑63                                                       TTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAA                                            <  2:1243509/91‑1                                                                  CATTTCGCCACTTATACAAAACAAAGTGAGTGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGA                                 <  2:1809333/91‑1                                                                                          ggcGAGTGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGACTGATAATTTGGACTAAACGCAAAATGA         >  2:998388/4‑91                                                                                             GAGTGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATC      <  2:1366759/91‑1                                                                                              AGTGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCA     <  2:1451556/91‑1                                                                                               GTGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCAT    >  2:3392/1‑91                                                                                                TGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATA   >  2:1044216/1‑91                                                                                                TGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATA   >  1:2862813/1‑91                                                                                                TGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATA   >  1:2776805/1‑91                                                                                                TGCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATA   >  1:1442647/1‑91                                                                                                 GCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATAG  <  1:114672/91‑1                                                                                                                                                                                             ATTGTTACTAACAGTAATGAAATAATCTATGATTCATTTTGCGTTTAGTCCAAATTATCAATCAACATTTCGCCACTTATACAAAACAAAGTGAGTG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2751278‑2751374 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtgagtgCCATTGTAAGAACACAAGACACTCACTTTGTTTTGTATAAGTGGCGAAATGTTGATTGATAATTTGGACTAAACGCAAAATGAATCATAG  <  USA300TCH1516_ALE/2751393‑2751304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ 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.