New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1283492	181 (0.950)	17 (0.100)	8/138	NT	9.1%	coding (57/4317 nt)	polC_1	DNA polymerase III PolC‑type
	?	USA300TCH1516_ALE	= 1283506	184 (1.120)					coding (71/4317 nt)	polC_1	DNA polymerase III PolC‑type

GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1283392‑1283492 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttaaaatttcaGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAAT  <  USA300TCH1516_ALE/1283506‑1283417                                                                                                                                                                                                 GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAAT                                                                                                      <  1:1146833/91‑1 GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAAT                                                                                                      <  1:1148785/91‑1 GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAAT                                                                                                      <  2:3511450/91‑1 GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAAT                                                                                                      >  1:1338252/1‑91 GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAAT                                                                                                      <  2:3511282/91‑1  TTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGGAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATT                                                                                                     <  2:3000167/91‑1  TTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATT                                                                                                     <  1:3673888/91‑1   TCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTA                                                                                                    <  1:895274/91‑1    CGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAA                                                                                                   <  2:2834928/91‑1    CGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAA                                                                                                   <  1:1084836/91‑1    CGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAA                                                                                                   <  2:2835042/91‑1    CGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAA                                                                                                   <  2:3662042/91‑1    CGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAA                                                                                                   <  2:2834894/91‑1     GAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAA                                                                                                  <  2:1728569/91‑1     GAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAA                                                                                                  <  2:1728558/91‑1     GAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAA                                                                                                  <  2:3474079/91‑1     GAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAA                                                                                                  <  2:3593858/91‑1        CACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATT                                                                                               <  2:3078561/91‑1        CACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATT                                                                                               <  2:3874650/91‑1          CGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTC                                                                                             <  1:2229604/91‑1           GTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCA                                                                                            >  1:2637100/1‑91           GTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCA                                                                                            >  2:3049094/1‑91           GTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCA                                                                                            >  1:3637594/1‑91           GTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCA                                                                                            >  1:1673766/1‑91                              AAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAA                                                                         <  2:3160936/91‑1                                 GTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTT                                                                      <  1:2751322/91‑1                                 GTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTT                                                                      <  2:2825389/91‑1                                 GTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTT                                                                      <  1:1765416/91‑1                                 GTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTT                                                                      <  2:548643/91‑1                                  TGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTT                                                                     <  1:1798670/91‑1                                   GGTAATTGTCTTGGCAATGACAGAGCAACAAGAATTTAAAGTGCGTGCTGATCGAATGAAAATTTCAGCATCTAATTGATTTGAAATTTTA                                                                    <  1:3096678/91‑1                                   GGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTA                                                                    <  1:264699/91‑1                                   GGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTA                                                                    <  1:539560/91‑1                                      AATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAATTTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATT                                                                 <  1:19004/91‑1                                      AATTGTCTGGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATT                                                                 <  2:2484326/91‑1                                       ATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTT                                                                <  2:263231/91‑1                                       ATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTT                                                                <  2:263919/91‑1                                       ATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTT                                                                <  1:1829150/91‑1                                               GGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCA                                                        <  1:2353217/91‑1                                                      ACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTT                                                 <  1:288048/91‑1                                                      ACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTT                                                 <  1:287879/91‑1                                                                                           TTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTAC            >  2:1521265/1‑91                                                                                           TTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTAC            <  2:470444/91‑1                                                                                           TTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTAC            <  1:2118155/91‑1                                                                                           TTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTAC            <  2:470508/91‑1                                                                                           TTAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAAGTAC            >  1:3003953/1‑91                                                                                            TAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACC           <  1:1568711/91‑1                                                                                            TAAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACC           <  1:1568646/91‑1                                                                                             AAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCA          >  1:3664688/1‑91                                                                                             AAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCA          <  1:2243492/91‑1                                                                                             AAAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCA          <  1:2265897/91‑1                                                                                             AAAATTTCAGCAGCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCA          <  2:3226952/91‑1                                                                                              AAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCAC         >  1:740616/1‑91                                                                                              AAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCAC         >  2:644353/1‑91                                                                                              AAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCAC         <  1:3666771/91‑1                                                                                              AAATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCAC         <  1:1796290/91‑1                                                                                               AATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACC        >  2:1557364/1‑91                                                                                               AATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACC        >  2:979824/1‑91                                                                                               AATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACC        <  1:241938/91‑1                                                                                                ATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCT       <  1:3202808/91‑1                                                                                                ATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCT       >  2:3770512/1‑91                                                                                                ATTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCT       <  2:2499649/91‑1                                                                                                 TTTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTT      >  1:2450769/1‑91                                                                                                  TTCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTA     <  1:40178/91‑1                                                                                                   TCAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAA    >  1:1280541/1‑91                                                                                                    CAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAA   >  1:147150/1‑91                                                                                                    CAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAA   >  1:3430256/1‑91                                                                                                    CAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAA   >  1:3430308/1‑91                                                                                                    CAGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAA   >  1:1490347/1‑91                                                                                                     AGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAAT  <  1:3838811/91‑1                                                                                                                                                                                                 GTTCGAACACGTAAAAGTAATTTCTATTTAAGGTGGTAATTGTCTTGGCAATGACAGAGCAACAAAAATTTAAAGTGCTTGCTGATCAAATTAAAATTTCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  USA300TCH1516_ALE/1283392‑1283492 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ttaaaatttcaGCATCTAATTGATTTGAAATTTTAATTTGATCAGCAAGCACTTTAAATTTTTGTTGCTCTGTCATTGCCAAGACAATTACCACCTTAAAT  <  USA300TCH1516_ALE/1283506‑1283417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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.