New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	1755658 =	37 (0.650)	3 (0.060)	3/242	NT	7.9%	intergenic (‑55/+300)	USA300HOU_1643/rpmA	GTP‑binding protein/ribosomal protein L27
	?	CP000730	1755694 =	36 (0.680)					intergenic (‑91/+264)	USA300HOU_1643/rpmA	GTP‑binding protein/ribosomal protein L27

CACCATCACCGGCTTTAAGAGATATTTTGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGATTAGGGGCTCTTATAC  >  CP000730/1755558‑1755830                                                                                                                                           |                                                                                                                                          cgccgggaCCGGCTTTAGTAGTTATTTTGAGTTGATCTACAAACATATATGTCACCTCGTTTACATATAATTTTCATTTTCCTAATAATTATAGCATATTAGAGCCCTTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGc                                                                                                                                       <  2:500840/134‑1 (MQ=255)    caTCACCGGCTTTAAGAGATATTTTGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGt                                                                                                                                    <  2:400937/141‑1 (MQ=255)         atacgggtgcagcgtttaaagaataaactgtaccacaattggtgctgagaaatataagtattttaaagcaaagatttataaaagtaactgcataagagccccttatatattgtaaataattaggggctctTATGCAGTTAc                                                                                                                                 <  2:28747‑M2/11‑1 (MQ=255)              tttAAGAGATATTTTGACTTGAGCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTtata                                                                                                                          <  1:249173/141‑1 (MQ=255)                 aaGAGATATTTTGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAAt                                                                                                                       >  2:279923/1‑141 (MQ=255)                  agatATATTTTGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTG‑ATTA‑TTATGAGGCCCTTTTGCAGTTACTTTTATAAAtt                                                                                                                      >  2:505794/1‑140 (MQ=255)                  agagATATTTTGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATc                                                                                                                      <  2:660033/141‑1 (MQ=255)                        atTTTGACTTGATCGACAAACATATAACTCACCTGTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCTCCTTAGATATTGTT‑AATA‑ATTAGGGGCTCTTATGCAGCTACTTTTATAAATCTTTGC‑t                                                                                                               <  1:405754/141‑1 (MQ=255)                            tGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATCTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTaa                                                                                                           >  2:365175/1‑141 (MQ=255)                            tGACCTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTGTTATGCAGTTACTCTTATAAATCTTTGC‑TTTaa                                                                                                           >  1:454295/1‑141 (MQ=255)                             gACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTaaa                                                                                                          >  2:647865/1‑141 (MQ=255)                                 actgtaccacaattggtgctgagaaatataagtattttaaagcaaagatttataaaagtaactgcataAGAGCCCCTAAT‑TATTTAA‑AATATATAAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATAc                                                                                                      <  1:198253‑M1/73‑1 (MQ=255)                                  gctctataaaCATATATCACACCTTCTTTACTTATAATTTTCACTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATCTTGTA‑AATA‑ATTAGGGGCTCTTATGCAGATACTTTTATAAATCTTTGC‑TTTAAAATACt                                                                                                     <  2:163439/134‑1 (MQ=255)                                  gATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACt                                                                                                     >  2:272881/1‑141 (MQ=255)                                  gATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAAAAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCCGTTACTTTTATAAATCTTTGC‑TTTAAAATACt                                                                                                     >  2:571383/1‑141 (MQ=255)                                   actgtaccacaattggtgctgagaaatataagtattttaaagcaaagatttataaaagtaactgcataagagccccttatatattgtaaataattaggggctctTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATAc                                                                                                      >  2:198253‑M2/105‑141 (MQ=255)                                                          ctTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGCTTTTAAAATACTTATATTTCTCAGCACCAATtgtg                                                                              >  2:127555/1‑141 (MQ=255)                                                               aCATATAATTTTCATTTTCCCAGTAATTATAGCATATTAGAGCCCCTTATATCTTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAACACGTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAg                                                                        >  1:452844/1‑141 (MQ=255)                                                                gtattttaaagcaaagatttataaaagtaactgcataAGAGCCCCTAAT‑TATTTAC‑AATATATAAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGt                                                                       >  2:198253‑M1/38‑141 (MQ=255)                                                                  gtattttaaagcaaagatttataaaagtaactgcataagagccccttatatattttaaataattaggggctctTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGt                                                                       <  1:198253‑M2/68‑1 (MQ=255)                                                                   ataATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCATCACCAATTGTGGTACAGTTTa                                                                    <  1:662783/141‑1 (MQ=255)                                                                   ataATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTa                                                                    >  1:178335/1‑141 (MQ=255)                                                                       ttttcattttcCCAATACTTATAGCATATTAGAGCCCCTTATCGATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTAATTTTATTAATAATGCA‑TTTAAAATGCTTGACGTTCTCAGCACCAATTGTGGTACAGTTTATTCt                                                                <  2:471133/141‑1 (MQ=255)                                                                       ttttcattttcCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCt                                                                <  1:152384/141‑1 (MQ=255)                                                                        tttcattttcCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCtt                                                               <  1:620484/141‑1 (MQ=255)                                                                              tttcCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACg                                                         >  1:357420/1‑141 (MQ=255)                                                                                 cccAATAATTATAGCATATTAGAGCCCCTTATATATTGTC‑AATA‑ATAAATAATACAAATGCAGAAAATGATACGAGTCGTTGC‑TTTAAAATATTGATATTTCTCTGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTg                                                      >  1:658557/1‑141 (MQ=255)                                                                                     ataatTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAAc                                                  <  1:279923/141‑1 (MQ=255)                                                                                     ataatTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAAc                                                  <  1:609289/141‑1 (MQ=255)                                                                                      aaatTATACCTTTTTAGGGCCCC‑TATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTg                                                <  1:121185/140‑1 (MQ=255)                                                                                          gtaactgcataAGAGCCCCTAAT‑TATT‑TACAATATATAAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCACCCGTAt                                             <  2:28747‑M1/130‑1 (MQ=255)                                                                                             aGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTcc                                          <  2:85913/141‑1 (MQ=255)                                                                                               cagatTAGTGCCCCTTTTTGATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAAGCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCtt                                        <  1:59116/138‑1 (MQ=255)                                                                                               cATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCTATTGTGGTACAGTTTATTCTTTAAACGCTCCAACTGTATTCCtt                                        <  1:365175/141‑1 (MQ=255)                                                                                               cATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCtt                                        <  2:665202/141‑1 (MQ=255)                                                                                                 tatTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTg                                      <  2:71714/141‑1 (MQ=255)                                                                                                  atTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGt                                     <  1:380177/141‑1 (MQ=255)                                                                                                   ttAGAGCCCCTTATATATTGGA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTc                                    <  2:662272/141‑1 (MQ=255)                                                                                                      GAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTcccc                                 >  1:411332‑M1/1‑141 (MQ=255)                                                                                                       AGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTGTTCCTTTGTccccc                                <  1:180950‑M1/141‑1 (MQ=255)                                                                                                       AGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATGCCTTTGTccccc                                <  1:180953‑M1/141‑1 (MQ=255)                                                                                                        GCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCt                               >  1:412647‑M1/1‑141 (MQ=255)                                                                                                        GCCCCTTATATATTGTA‑AATA‑ATCAGGGACTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATAACTCTGCACCAATTGCGGTACAGTTTATTCTTTAAACGCTGCAAATGGATTCCTTTGTCCCCCt                               <  2:267972‑M1/141‑1 (MQ=255)                                                                                                        GCCCCCTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTACACGCTGCAACTGTATTCCTTTGTCCCCCt                               >  1:361133‑M1/1‑141 (MQ=255)                                                                                                           CCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTtat                            >  2:174521‑M1/1‑141 (MQ=255)                                                                                                           CCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTtat                            <  2:255477‑M1/141‑1 (MQ=255)                                                                                                             ttttatatTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTGTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAg                          <  2:181765/138‑1 (MQ=255)                                                                                                              tatataTTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTGTAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGt                         >  2:184397/1‑141 (MQ=255)                                                                                                              tatataTTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGt                         >  2:184407/1‑141 (MQ=255)                                                                                                              tatataTTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGt                         >  1:362290/1‑141 (MQ=255)                                                                                                                       aa‑aaTA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGAtt                <  2:85855/140‑1 (MQ=255)                                                                                                                                ttAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGATTAGGGGct         >  1:653003/1‑141 (MQ=255)                                                                                                                                   ggggctctTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTATCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGATTAGGGGCTCtt      >  1:447492‑M2/9‑141 (MQ=255)                                                                                                                                     ggctctCATGCAGTTACTTTTATAAATCTTTGC‑TTTCAAATACCTATACTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAATGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGATTAGGGGCTCTtat    <  1:555433‑M2/135‑1 (MQ=255)                                                                                                                                       ctctTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGATTAGGGGCTCTTATAc  >  1:3082‑M2/5‑141 (MQ=255)                                                                                                                                           |                                                                                                                                          CACCATCACCGGCTTTAAGAGATATTTTGACTTGATCGACAAACATATATCTCACCTCTTTTACATATAATTTTCATTTTCCCAATAATTATAGCATATTAGAGCCCCTTATATATTGTA‑AATA‑ATTAGGGGCTCTTATGCAGTTACTTTTATAAATCTTTGC‑TTTAAAATACTTATATTTCTCAGCACCAATTGTGGTACAGTTTATTCTTTAAACGCTGCAACTGTATTCCTTTGTCCCCCTTATAGTTTAGTGATTAGGGGCTCTTATAC  >  CP000730/1755558‑1755830

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ 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.