New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2854319	334 (1.160)	10 (0.040)	9/150	NT	2.9%	intergenic (+17/+396)	yflS/USA300HOU_RS14625	Putative malate transporter YflS/hypothetical protein
	?	USA300TCH1516_ALE	= 2854338	359 (1.330)					intergenic (+36/+377)	yflS/USA300HOU_RS14625	Putative malate transporter YflS/hypothetical protein
Rejected: Frequency below/above cutoff threshold.

TTAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2854225‑2854319 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agcgcCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  <  USA300TCH1516_ALE/2854338‑2854249                                                                                                                                                                                           TTAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTA                                                                                                >  2:3006406/1‑91  TAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAG                                                                                               <  2:4327229/91‑1  TAATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAG                                                                                               >  1:4016271/1‑91   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  2:3066613/1‑91   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  1:1497380/1‑91   AATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGC                                                                                              >  1:5173264/1‑91    ATATTAGGTTTCGTCTACTTTATTATCTTGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCG                                                                                             <  1:4537902/91‑1    ATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCG                                                                                             <  2:2952025/91‑1    ATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCG                                                                                             <  2:1326399/91‑1    ATATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCG                                                                                             >  1:3681387/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            >  2:3217933/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            >  1:5309415/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            <  2:4659782/91‑1     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            <  1:2935705/91‑1     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            >  2:68331/1‑91     TATTAGGTTTCGTCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGC                                                                                            <  1:2935463/91‑1                 TCTACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGA                                                                                <  1:5415087/91‑1                    ACTTTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGAT                                                                             <  2:1536527/91‑1                       TTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCG                                                                          <  1:5359771/91‑1                       TTATTATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCG                                                                          <  1:5359750/91‑1                           TATCTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCG                                                                      <  1:2503541/91‑1                              CTGGATTGGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTA                                                                   <  1:5104269/91‑1                                     GGTTTAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAA                                                            <  1:3409531/91‑1                                         TAGGATCACTTTGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATAAATGAGATTCGAGCGCTAATTTAAATATT                                                        <  2:4264631/91‑1                                                    TGGATGAAAGTAATTGGTATATTTTAAAATATTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATAC                                             <  1:1055307/91‑1                                                                                   TTTAAATTAGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACC              <  1:2115560/91‑1                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      <  1:2091523/91‑1                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      >  1:1417983/1‑91                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      >  2:2290894/1‑91                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      >  1:962179/1‑91                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      >  2:5003269/1‑91                                                                                           AGCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGA      >  2:4959247/1‑91                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     <  1:1764067/91‑1                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  1:557952/1‑91                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  2:4719037/1‑91                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  1:2731909/1‑91                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     <  1:39215/91‑1                                                                                            GCGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGAT     >  1:3164001/1‑91                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCGGATA    <  1:5316511/91‑1                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    >  2:4098631/1‑91                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    >  2:675506/1‑91                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    >  2:992147/1‑91                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    >  2:2239149/1‑91                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    >  1:2744/1‑91                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    <  1:1534245/91‑1                                                                                             CGCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATA    >  1:135441/1‑91                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTCAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   >  2:3600575/1‑91                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAGATATACCAATTACTTTCGTCTAAAGTGATCCTAATCCAATCCAGATAA   <  1:4487932/91‑1                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   >  1:5166157/1‑91                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   <  1:4942263/91‑1                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   >  1:2347002/1‑91                                                                                              GCCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAA   >  1:1220776/1‑91                                                                                               CCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  >  2:3935538/1‑91                                                                                               CCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  <  1:456383/91‑1                                                                                               CCCAAATCAATGAGATTCGAGCGCTAATTTAAATATTTTAAAATATACCAATTACTTTCATCCAAAGTGATCCTAAACCAATCCAGATAAT  >  2:5371251/1‑91                                                                                                                                                                                           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 < 22 ≤ 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.