New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	693013 =	48 (0.880)	3 (0.060)	3/248	3.4	5.9%	intergenic (‑40/+135)	USA300HOU_0635/USA300HOU_0636	possible replication initiation protein/hypothetical protein
	?	CP000730	693128 =	52 (1.030)					intergenic (‑155/+20)	USA300HOU_0635/USA300HOU_0636	possible replication initiation protein/hypothetical protein
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GTGACCTGAACCCAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAAC  >  CP000730/692876‑693153                                                                                                                                          |                                                                                                                                             gTGACCTGAACCCAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACAt                                                                                                                                           <  2:151970/141‑1 (MQ=255)   gACCTGAACCCAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGa                                                                                                                                         >  2:533353/1‑141 (MQ=255)         aaCCCAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTtc                                                                                                                                   <  1:302425/141‑1 (MQ=255)         aaCCCAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTtc                                                                                                                                   <  1:593753/141‑1 (MQ=255)           cccAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTtctc                                                                                                                                 >  2:148244/1‑141 (MQ=255)            ccAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCg                                                                                                                                <  2:433489/141‑1 (MQ=255)             cAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGc                                                                                                                               <  1:309401/141‑1 (MQ=255)               gTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCtt                                                                                                                             >  1:95365/1‑141 (MQ=255)                    caacTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTa                                                                                                                        >  1:346923/1‑141 (MQ=255)                     aacTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTaa                                                                                                                       >  1:7280/1‑141 (MQ=255)                       cTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAAcg                                                                                                                     >  1:557181/1‑141 (MQ=255)                          ccTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGt                                                                                                                  <  2:41333/141‑1 (MQ=255)                           cTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTa                                                                                                                 >  2:124966/1‑141 (MQ=255)                                caGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGt                                                                                                            >  2:139445/1‑141 (MQ=255)                                       tttATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGc                                                                                                     <  1:113303/141‑1 (MQ=255)                                                 cGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCaaa                                                                                           <  1:56513/141‑1 (MQ=255)                                                   ctctACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGAc                                                                                                                                        <  2:76946/94‑1 (MQ=255)                                                   ctctACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGAc                                                                                                                                        >  1:76946/1‑94 (MQ=255)                                                           cccTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGc                                                                                 <  1:588934/141‑1 (MQ=255)                                                           cccTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGATTTCCTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGc                                                                                 <  1:148244/141‑1 (MQ=255)                                                                ttAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTcc                                                                            <  1:84557/141‑1 (MQ=255)                                                                    tAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGc                                                                        >  2:620343/1‑141 (MQ=255)                                                                     aaGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCt                                                                       <  2:345656/141‑1 (MQ=255)                                                                         ggggTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCa                                                                   <  2:617622/141‑1 (MQ=255)                                                                             tACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCTGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTc                                                               <  1:533353/141‑1 (MQ=255)                                                                             tACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTc                                                               >  1:307347/1‑141 (MQ=255)                                                                                 cTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTgcg                                                           >  1:75495/1‑141 (MQ=255)                                                                                        tttAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCAt                                                    <  1:438140/141‑1 (MQ=255)                                                                                         ttAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCCTa                                                   >  1:504525/1‑141 (MQ=255)                                                                                          tAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATAc                                                  >  1:275246/1‑141 (MQ=255)                                                                                            aaGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGc                                                <  1:214750/141‑1 (MQ=255)                                                                                              gTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTa                                              <  2:346923/141‑1 (MQ=255)                                                                                                          tatGCCTCCTATCAGATCGCAAGCGATTTGTTACATGCCCGCTCTCGATTTTTTAACGCGTATTTGTGGCAGGCTCCGCCCAAATGCTTAACGCATACCGTGCGTGAATGTCTGCGCATGCATACGCTATAAGCTACGCgg                                  <  2:72406/141‑1 (MQ=255)                                                                                                          tatGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACgg                                  <  1:548792/141‑1 (MQ=255)                                                                                                            tGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTc                                <  1:124966/141‑1 (MQ=255)                                                                                                             gCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTTATTCTTTTTTTTCTCATTCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCa                               >  2:556959/1‑141 (MQ=255)                                                                                                             gCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCa                               >  1:278650/1‑141 (MQ=255)                                                                                                               ctcctATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATg                             <  1:139445/141‑1 (MQ=255)                                                                                                                tcctATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGt                            >  1:215906/1‑141 (MQ=255)                                                                                                                    aTCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTaaa                        >  1:326097/1‑141 (MQ=255)                                                                                                                             cAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATa               >  2:247298/1‑141 (MQ=255)                                                                                                                              aaGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATAc              >  1:257530/1‑141 (MQ=255)                                                                                                                                gCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACta            <  1:620343/141‑1 (MQ=255)                                                                                                                                   aTTTGATACATGACCGTTCTCGCTTTTTTATTTTTTTTTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTatat         >  2:117174/1‑141 (MQ=255)                                                                                                                                   aTTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTatat         <  2:249848/141‑1 (MQ=255)                                                                                                                                   aTTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTatat         <  2:7280/141‑1 (MQ=255)                                                                                                                                      tGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGtt      >  1:151638/1‑141 (MQ=255)                                                                                                                                       gATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTa     >  1:103613/1‑141 (MQ=255)                                                                                                                                          aCATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTCGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGCTacac  >  2:69814/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                             GTGACCTGAACCCAGTCAACAACTGCCTCCACAGCACTTTTATTTGTACGCTCTACCCCCCTATTAGTAAGGGGGGTACACTGGTTTTTTAAAGTCATATTTATTTATGCCTCCTATCAAATCGCAAGCGATTTGATACATGACCGTTCTCGCTTTTTTAACGCGTATTTGTCGCAGGCTCCGCCCAAATGCTTAACGCACTCCGTGCTTGCATTTCTGCGCCTGCATACGCTAAAAGCTACACGGTCATGTTAAATCACTAATACTATATGTTAAAC  >  CP000730/692876‑693153

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.