New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	895785 =	26 (0.730)	8 (0.260)	3/246	3.2	22.6%	coding (806/822 nt)	metQ_2	Methionine‑binding lipoprotein MetQ
	?	USA300TCH1516_ALE	= 909740	32 (1.020)					intergenic (‑663/‑371)	USA300HOU_RS04500/csbD_1	hypothetical protein/Stress response protein CsbD
Rejected: Coverage evenness skew score above cutoff.

TGGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCA  >  USA300TCH1516_ALE/909600‑909870                                                                                                                                             |                                                                                                                                   tgGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTaa                                                                                                                                    <  1:250404/141‑1 (MQ=255)   gttgttTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAatt                                                                                                                                  <  1:210761/141‑1 (MQ=255)             aGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCta                                                                                                                        >  1:62395/1‑141 (MQ=255)                  caaaaaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGGGTATAGAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCtaaataa                                                                                                                   >  1:392726/2‑141 (MQ=255)                  aaaaaaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCtaaataa                                                                                                                   >  2:49398/1‑141 (MQ=255)                  aaaaaaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCtaaataa                                                                                                                   >  2:111645/1‑141 (MQ=255)                    aaaaaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTaaataaat                                                                                                                 <  1:29375/141‑1 (MQ=255)                       aaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCat                                                                                                              <  1:187017/141‑1 (MQ=255)                       aaGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCat                                                                                                              <  2:100621/141‑1 (MQ=255)                       aaGGGCATAATTTTGAAACAAAGGGCAAGGGGATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCat                                                                                                              <  2:239218/141‑1 (MQ=255)                        aGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCata                                                                                                             <  1:405412/141‑1 (MQ=255)                         gggCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCatat                                                                                                            >  2:265849/1‑141 (MQ=255)                         gggCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCatat                                                                                                            >  2:142901/1‑141 (MQ=255)                         gggCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATGTTATAAATGCATATATAACAATGTTTTGATTGGCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCCGCTAAATAcatcatgt                                                                                                            >  2:241332/1‑139 (MQ=255)                                  tttGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTc                                                                                                   >  1:164246/1‑141 (MQ=255)                                  tttGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAAGTTTATAAATGCGTATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTc                                                                                                   >  2:351234/1‑141 (MQ=255)                                       aaCAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTaa                                                                                              >  1:345682/1‑141 (MQ=255)                                           aaGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTg                                                                                          <  2:134529/141‑1 (MQ=255)                                           aaGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTg                                                                                          <  2:177632/141‑1 (MQ=255)                                           aaGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTg                                                                                          <  1:193616/141‑1 (MQ=255)                                               gCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGt                                                                                      <  2:412294/141‑1 (MQ=255)                                                 aaGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTTCCGTGATGTTg                                                                                    <  2:323072/141‑1 (MQ=255)                                                 aaGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTg                                                                                    <  2:57331/141‑1 (MQ=255)                                                 aaGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTg                                                                                    <  1:331067/141‑1 (MQ=255)                                                     gTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTgg                                                                                <  2:40426/141‑1 (MQ=255)                                                     gTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTgg                                                                                <  2:396405/141‑1 (MQ=255)                                                           ataataAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCtttt                                                                          <  1:48017/141‑1 (MQ=255)                                                                   ttATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTtttaatttaa                                                                  >  2:263085/1‑141 (MQ=255)                                                                    tATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTaaa                                                                 <  2:381496/141‑1 (MQ=255)                                                                                   ataAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGa                                                  >  1:274395/1‑141 (MQ=255)                                                                                     aaaTGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGata                                                <  2:119313/141‑1 (MQ=255)                                                                                                 aaCAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATgag                                    <  1:171739/141‑1 (MQ=255)                                                                                                 aaCAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATgag                                    <  1:124324/141‑1 (MQ=255)                                                                                                           tGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTAc                          >  2:88483/1‑141 (MQ=255)                                                                                                            gATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACg                         <  1:389319/141‑1 (MQ=255)                                                                                                                  ccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAACTAAATCATATTAATGGCTCAGTACCGTGATGTTGCTCGGATTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATaaa                   <  1:351234/141‑1 (MQ=255)                                                                                                                  ccTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATaaa                   <  2:164246/141‑1 (MQ=255)                                                                                                                                   aaTCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATatgca  <  1:274962/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                   TGGTTGTTTTCAAGGGCAAAAAAAGGGCATAATTTTGAAACAAAGGGCAAGGGTATGAATAATAAATTATCTTGAAAATTTTATAAATGCATATATAACAATGTTTTGATTGCCCTTGAACTTCCTTGATAATCTGGCTAATTATTCCTGCTAAATAAATCATATTAATGGCTCAGTAACGTGATGTTGCTGGGCTTTTTAATTTAAACAGGTATTTATATGATATTTAGGAATGAGATGCTATTACGGATAAAGTAAAATCCTATATGCA  >  USA300TCH1516_ALE/909600‑909870

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.