New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1255979	165 (0.810)	27 (0.160)	12/134	NT	15.5%	intergenic (+195/+49)	rplS/USA300HOU_RS06250	50S ribosomal protein L19/hypothetical protein
	?	USA300TCH1516_ALE	= 1255992	157 (0.920)					intergenic (+208/+36)	rplS/USA300HOU_RS06250	50S ribosomal protein L19/hypothetical protein

TTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1255877‑1255979 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaatctactaagtCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATTAT  <  USA300TCH1516_ALE/1255992‑1255903                                                                                                                                                                                                   TTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAA                                                                                                        >  1:1204031/1‑91 TTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAA                                                                                                        >  1:1527905/1‑91  TTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAA                                                                                                       >  1:1100326/1‑91   TGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATACAAACAAAAA                                                                                                      <  1:625296/91‑1    GCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAAT                                                                                                     >  2:3885296/1‑91    GCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAAT                                                                                                     >  2:1278319/1‑91    GCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTATATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAAT                                                                                                     >  2:418236/1‑91     CTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATC                                                                                                    <  2:715894/91‑1     CTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATC                                                                                                    >  1:2704964/1‑91     CTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATC                                                                                                    <  1:137265/91‑1     CTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATC                                                                                                    >  1:3861530/1‑91      TGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCT                                                                                                   >  2:2212287/1‑91      TGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCT                                                                                                   >  1:599504/1‑91      TGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCT                                                                                                   >  2:1620029/1‑91      TGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCT                                                                                                   >  2:2212392/1‑91        TTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTAC                                                                                                 >  1:3139414/1‑91        TTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTAC                                                                                                 <  1:2139210/91‑1         TTAGTTAATGTAAAGTTGATTATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACT                                                                                                >  1:696888/1‑91         TTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACT                                                                                                <  2:983099/91‑1         TTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACT                                                                                                >  1:539494/1‑91         TTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACT                                                                                                <  2:2220722/91‑1          TAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTA                                                                                               <  1:722294/91‑1           AGTTAATGTAAAGTTGATAATGTAATTGTTTCTTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGCTTATATAAACACAAATCTACTAA                                                                                              >  2:3015197/1‑91           AGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAA                                                                                              <  2:3142276/91‑1            GTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAG                                                                                             >  1:3468858/1‑91            GTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAG                                                                                             >  1:3468895/1‑91             TTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGT                                                                                            <  1:826661/91‑1                       GTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAAT                                                                                  <  2:3305790/91‑1                        TTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATG                                                                                 <  2:4825/91‑1                        TTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAAAAAAAATCTACTAAGTCCTTTTCAATG                                                                                 <  2:1471990/91‑1                         TGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGG                                                                                <  2:2558109/91‑1                         TGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGG                                                                                <  1:3880698/91‑1                          GATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGC                                                                               <  2:3758384/91‑1                           ATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCA                                                                              <  1:209287/91‑1                            TAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCAC                                                                             <  1:3421022/91‑1                              ATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTT                                                                           <  1:2112687/91‑1                              ATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTT                                                                           <  2:1276054/91‑1                               TGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTA                                                                          <  1:2827370/91‑1                               TGTAAGTGTTTATGCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGGCCTTTTCAATGGCACTga                                                                          <  2:44281/91‑3                                gcAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  2:2324501/89‑1                                GTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  2:3486393/91‑1                                GTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  1:1700643/91‑1                                GTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  2:2078797/91‑1                                GTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  1:1986565/91‑1                                GTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  1:1853397/91‑1                                GTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAG                                                                         <  1:517188/91‑1                                 TAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCTTTTTCAATGGCACTTAGT                                                                        <  1:1750621/91‑1                                 TAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCTTTTTCAATGGCACTTAGT                                                                        <  1:1750863/91‑1                                 TAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCTTTTTCAATGGCACTTAGT                                                                        <  1:1750889/91‑1                                 TAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAGT                                                                        <  2:3492373/91‑1                                 TAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGACCTTTTCAATGGCACTTAGT                                                                        <  2:2981221/91‑1                                  AATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAGTA                                                                       <  1:1268014/91‑1                                   ATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAGTAG                                                                      <  2:902457/91‑1                                   ATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGTCCTTTTCAATGGCACTTAGTAG                                                                      <  1:1321364/91‑1                                                                                           AAATCTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAA              >  2:3721876/1‑91                                                                                           AAATCTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAA              <  2:2912199/91‑1                                                                                           AAATCTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAA              >  2:2085887/1‑91                                                                                             ATCTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATCACCATTTTGAGCAAACACGTTATGAATAGCGAAGGAATAAACA            >  1:3956251/1‑91                                                                                              TCTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAA           >  2:2979208/1‑91                                                                                              TCTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAA           >  2:1314744/1‑91                                                                                               CTACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAAT          >  2:205386/1‑91                                                                                                TACTAAGTCTTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATGAACAATT         >  1:1970924/1‑91                                                                                                 ACTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTA        >  2:1627219/1‑91                                                                                                  CTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTAC       <  1:1486365/91‑1                                                                                                  CTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTAC       >  2:3930114/1‑91                                                                                                  CTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTAC       <  1:1277158/91‑1                                                                                                  CTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTAC       >  2:1557245/1‑91                                                                                                  CTAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTAC       <  2:2194717/91‑1                                                                                                   TAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACA      <  1:1720461/91‑1                                                                                                   TAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACA      <  1:1720699/91‑1                                                                                                   TAAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACA      >  2:3250600/1‑91                                                                                                    AAGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACAT     >  2:3757432/1‑91                                                                                                    AAGGCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACAT     <  2:373429/91‑1                                                                                                     AGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACACTTACATT    >  2:3634459/1‑91                                                                                                     AGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATT    <  1:1146741/91‑1                                                                                                     AGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATT    <  1:331790/91‑1                                                                                                     AGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATT    >  1:1018595/1‑91                                                                                                     AGTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATT    <  2:2663016/91‑1                                                                                                      GTCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATTA   <  2:1483050/91‑1                                                                                                       TCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATTAT  <  1:3785804/91‑1                                                                                                       TCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATTAT  <  2:1798326/91‑1                                                                                                                                                                                                   TTTGCTGTTTAGTTAATGTAAAGTTGATAATGTAATTGTTTATTCCTTCTCTATTCATAACGTGTTTGCTCAAAATGGTTATATAAACAAAAATCTACTAAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1255877‑1255979 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaatctactaagtCCTTTTCAATGGCACTTAGTAGATTTTTGTTTATATAACCATTTTGAGCAAACACGTTATGAATAGAGAAGGAATAAACAATTACATTAT  <  USA300TCH1516_ALE/1255992‑1255903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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.