New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 2792627	131 (0.690)	23 (0.150)	13/132	NT	16.1%	intergenic (+78/+34)	yvyI/yueB	Putative mannose‑6‑phosphate isomerase YvyI/ESX secretion system protein YueB
	?	USA300TCH1516_ALE	= 2792641	132 (0.840)					intergenic (+92/+20)	yvyI/yueB	Putative mannose‑6‑phosphate isomerase YvyI/ESX secretion system protein YueB

GTGCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2792524‑2792627 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaatccacacattaGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATTGC  <  USA300TCH1516_ALE/2792641‑2792552                                                                                                                                                                                                         GTGCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑A                                                                                                         >  2:2529298/1‑91 GTGCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑A                                                                                                         <  2:2599495/91‑1 GTGCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑A                                                                                                         <  1:1217695/91‑1 GTGCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑A                                                                                                         >  2:1228447/1‑91   GCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAA                                                                                                       >  2:3183357/1‑91   GCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAA                                                                                                       >  1:1508228/1‑91   GCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAA                                                                                                       >  1:1508279/1‑91    CTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAAT                                                                                                      <  2:2261880/91‑1    CTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAAT                                                                                                      >  2:2529280/1‑91    CTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAAT                                                                                                      <  1:2782967/91‑1    CTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAAT                                                                                                      <  2:2158103/91‑1    CTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAAT                                                                                                      <  1:949420/91‑1     TATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATC                                                                                                     >  1:3792476/1‑91     TATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATC                                                                                                     >  1:208334/1‑91     TATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATC                                                                                                     <  2:73398/91‑1       TAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCA                                                                                                   <  1:1644138/91‑1       TAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCA                                                                                                   <  1:533170/91‑1       TAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCA                                                                                                   <  1:1109849/91‑1          TAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACAC                                                                                                >  1:3856867/1‑91          TAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACAC                                                                                                <  1:1094454/91‑1          TAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACAC                                                                                                <  1:748167/91‑1           AAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACA                                                                                               >  1:316574/1‑91           AAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACA                                                                                               >  2:3046327/1‑91           AAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACA                                                                                               >  1:3038119/1‑91            AGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACAT                                                                                              <  2:775827/91‑1             GTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATT                                                                                             >  1:1710152/1‑91                  CCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGT                                                                                        >  2:151716/1‑91                   CTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTT                                                                                       >  1:763694/1‑91                   CTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCA                                                                                                   <  2:2190180/79‑1                   CTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCA                                                                                                   >  1:2190180/1‑79                     GGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTAT                                                                                     <  1:13687/91‑1                       ATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAG                                                                                   <  2:2946200/91‑1                       ATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAG                                                                                   <  2:1702328/91‑1                            AGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCT                                                                              <  2:2843142/91‑1                            AGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCT                                                                              <  2:321061/91‑1                            AGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCT                                                                              <  2:3333321/91‑1                            AGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCT                                                                              <  2:3333402/91‑1                             GCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTT                                                                             <  2:1096780/91‑1                              CAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTA                                                                            <  2:67017/91‑1                              CAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTA                                                                            <  1:1028923/91‑1                               AATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAA                                                                           <  2:687079/91‑1                                ATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAAAAATTAAATCCACACATTAGGGTTATAGCTCC                                                                               <  1:2501517/91‑1                                 TGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATG                                                                         <  1:2255130/91‑1                                    TAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGT                                                                      <  1:3832/91‑1                                     AACAACCGTCCTATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTG                                                                     <  1:2431145/91‑1                                     AACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTG                                                                     <  1:1012034/91‑1                                     AACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTG                                                                     <  2:2395192/91‑1                                     AACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTG                                                                     <  1:1561628/91‑1                                      ACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGG                                                                    <  2:1592918/91‑1                                      ACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGG                                                                    <  2:1593006/91‑1                                      ACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGG                                                                    <  1:151716/91‑1                                       CAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGA                                                                   <  2:763694/91‑1                                                       GACAGAAATTGCTATCTCGTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGA                                                   <  2:240580/91‑1                                                                                                AAATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGG               >  2:1385861/1‑91                                                                                                 AATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGT              <  1:219176/91‑1                                                                                                 AATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGT              >  1:2534592/1‑91                                                                                                 AATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGT              <  1:3328094/91‑1                                                                                                 AATCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGT              <  1:3330312/91‑1                                                                                                   TCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTG            <  2:11095/91‑1                                                                                                   TCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTG            >  2:3786656/1‑91                                                                                                   TCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTG            <  2:141343/91‑1                                                                                                   TCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTG            <  2:2425352/91‑1                                                                                                   TCCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTCTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTG            >  1:1373056/1‑91                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  2:2884852/91‑1                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  2:544980/91‑1                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  2:2643937/91‑1                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  1:2281277/91‑1                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  1:1153773/91‑1                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           >  1:573939/1‑91                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           >  2:1848787/1‑91                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  2:2003979/91‑1                                                                                                    CCACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGT           <  2:2099516/91‑1                                                                                                     CACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTT          >  1:2858804/1‑91                                                                                                     CACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTT          >  1:3858202/1‑91                                                                                                     CACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTT          >  2:2271822/1‑91                                                                                                      ACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTA         >  1:3750303/1‑91                                                                                                      ACACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTA         <  1:3122986/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTTTGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:3501722/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTGTGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:3501594/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGCGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTAcc       >  2:1041889/1‑89                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:3028862/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  1:680192/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  1:1329808/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:2148417/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:3202831/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:2148297/91‑1                                                                                                        ACATTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATC       <  2:2148249/91‑1                                                                                                           TTAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATT    <  1:204563/91‑1                                                                                                            TAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATTG   <  2:944859/91‑1                                                                                                            TAGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGCCTTTTATGGGACGGTTGTTATCATTG   <  2:944881/91‑1                                                                                                             AGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATTGC  >  1:1557297/1‑91                                                                                                             AGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATTGC  >  1:3770951/1‑91                                                                                                             AGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATTGC  <  1:912289/91‑1                                                                                                                                                                                                         GTGCTATAGTAAGTCATCCTGGATAATAGCAATGATAACAACCGTCCCATAAAAGACAGAAATTACTATCTCTTCTGTCTAAAAACATAA‑‑‑‑‑AAATCCACACATTA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/2792524‑2792627 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑aaatccacacattaGGGTTATAGCTCCTTAATGTGTGGATTTTTATGTTTTTAGACAGAAGAGATAGTAATTTCTGTCTTTTATGGGACGGTTGTTATCATTGC  <  USA300TCH1516_ALE/2792641‑2792552

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.