New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2854319	190 (1.000)	25 (0.140)	14/150	NT	11.5%	intergenic (+17/+396)	yflS/USA300HOU_RS14625	Putative malate transporter YflS/hypothetical protein
	?	USA300TCH1516_ALE	= 2854338	208 (1.170)					intergenic (+36/+377)	yflS/USA300HOU_RS14625	Putative malate transporter YflS/hypothetical protein

TTAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2854225‑2854319 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agcgcCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  <  USA300TCH1516_ALE/2854338‑2854249                                                                                                                                                                                           TTAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTCGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTA                                                                                                <  2:3405019/91‑1 TTAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTA                                                                                                <  2:1457473/91‑1  TAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAG                                                                                               <  1:2075118/91‑1   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  2:1725363/1‑91   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  2:2785480/1‑91   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  2:1782817/1‑91   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  2:1901643/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            >  1:874776/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            >  2:2307118/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGATTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            <  1:3175592/91‑1             TTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCA                                                                                    <  1:2067370/91‑1                  CTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAG                                                                               <  2:1340022/91‑1                  CTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAG                                                                               <  2:1339593/91‑1                  CTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAG                                                                               <  2:1241405/91‑1                  CTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAG                                                                               <  2:1196506/91‑1                   TACTTTATTATCTGGATTGGTTTAGGATCACTTTGGGTGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGA                                                                              <  2:3061513/91‑1                   TACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGA                                                                              <  2:899594/91‑1                      TTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTC                                                                           <  1:784186/91‑1                       TTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCG                                                                          <  1:404598/91‑1                       TTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCG                                                                          <  1:3385347/91‑1                       TTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAA‑AAGCGCCCAAATCAATGAGATTCGA                                                                         <  2:849902/91‑1                        TATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGA                                                                         <  1:1276008/91‑1                         tTTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAG                                                                        <  2:1119031/90‑1                           TATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCG                                                                      <  1:598091/91‑1                           TATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCG                                                                      <  1:307725/91‑1                            ATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGC                                                                     <  2:1041653/91‑1                            ATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGC                                                                     <  1:3215880/91‑1                            ATCTGGATTAGTTTAGGATCACTTTGGATGATTGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGATATTCGAGCGC                                                                     <  2:426368/91‑1                             TCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCT                                                                    <  1:1611066/91‑1                              CTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTA                                                                   <  2:2476888/91‑1                                 GATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATT                                                                <  2:3783215/91‑1                                 GATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATT                                                                <  2:3781009/91‑1                                   TTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATTTA                                                              <  1:974601/91‑1                                     GGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTACATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAA                                                            <  2:2399485/91‑1                                     GGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTACATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAA                                                            <  2:465757/91‑1                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      >  1:3079081/1‑91                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      <  2:3465506/91‑1                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      <  2:1561054/91‑1                                                                                            GCGCCCAAATCTATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     <  1:3518508/91‑1                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     <  1:2325023/91‑1                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  2:3274999/1‑91                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  2:3811237/1‑91                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  2:587409/1‑91                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   <  2:1838786/91‑1                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   >  1:3530617/1‑91                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   >  1:3530926/1‑91                                                                                               CCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  >  1:1099420/1‑91                                                                                                                                                                                           TTAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2854225‑2854319 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agcgcCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  <  USA300TCH1516_ALE/2854338‑2854249

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