New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 1636407	106 (0.690)	21 (0.170)	9/146	NT	18.0%	intergenic (‑40/‑349)	nohQ/ynfO	pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage
	?	NC_000913	= 1636432	104 (0.830)					intergenic (‑65/‑324)	nohQ/ynfO	pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin/uncharacterized protein, Qin prophage

TGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1636294‑1636407 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agaaaggaaacgacagGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTT  <  NC_000913/1636432‑1636334                                                                                                                                                                                                                       TGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAG                                                                                                                   <  2:2199275/100‑1 TGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAG                                                                                                                   <  2:1746195/100‑1  GTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAACACAGAGA                                                                                                                  <  1:1290684/100‑1    TCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGCAAATGTCAGCCAGCTGCTTTTTGTTGACTTTCATTGTTCATTCCACGGCCAAAACCAGAGAA                                                                                                                 >  1:1224142/1‑99     CCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAG                                                                                                               <  2:3815279/100‑1     CCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAG                                                                                                               >  1:4106610/1‑100      CTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGG                                                                                                              <  1:1537995/100‑1      CTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGG                                                                                                              >  2:1909065/1‑100      CTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGG                                                                                                              >  1:46062/1‑100      CTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAA                                                                                                                >  1:99110/1‑98       TGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGA                                                                                                             >  2:4223536/1‑100       TGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGA                                                                                                             >  2:1042489/1‑100       TGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGG                                                                                                              <  1:900509/99‑1        GCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAA                                                                                                            >  2:188395/1‑100          CAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAAC                                                                                                          >  2:111341/1‑100          CAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAAC                                                                                                          <  2:1869099/100‑1          CAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAAC                                                                                                          >  2:688467/1‑100          CAGTTCTGAATGATACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAAC                                                                                                          >  2:2806548/1‑100              TCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACA                                                                                                      >  1:858000/1‑100              TCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACA                                                                                                      >  2:47748/1‑100              TCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACA                                                                                                      >  2:4095935/1‑100              TCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACA                                                                                                      >  2:3939244/1‑100                                                AGCCAGCTGCTTTATGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTT                                                                    <  1:3608443/100‑1                                                 GCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTT                                                                   >  2:3950470/1‑100                                                 GCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTT                                                                   <  2:2237942/100‑1                                                 GCCAGCTGCTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTT                                                                   <  1:1996899/100‑1                                                 GCCAGCTGCTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTT                                                                   <  2:1020688/100‑1                                                  CCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTC                                                                  <  1:3950451/100‑1                                                  CCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTC                                                                  <  2:2266405/100‑1                                                  CCAGCTGCTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTC                                                                  <  2:169169/100‑1                                                   CAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCC                                                                 <  2:1245817/100‑1                                                   CAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCC                                                                 <  1:1940696/100‑1                                                   CAGCTGCTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCC                                                                 <  2:2785025/100‑1                                                   CAGCTGCTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCC                                                                 <  2:529919/100‑1                                                   CAGCTACTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCC                                                                 <  2:1490542/100‑1                                                    AGCTGCTTTTTGTTGACTTCCATTTCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCCT                                                                <  1:1570847/100‑1                                                    AGCTGCTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCCT                                                                <  1:2006287/100‑1                                                     GCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTT                                                               <  2:2876634/100‑1                                                       TGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTC                                                             <  2:2329444/100‑1                                                         CTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCCTTTCTC                                                           <  2:2078858/100‑1                                                         CTTTTTGTTGACTTCCATTGCACATTCCACGGACAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAGCGAGCTTTTTGGCCTCTGTCGTTTCCTTTCTC                                                           <  1:83401/100‑1                                                           TTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTG                                                         <  2:1830122/100‑1                                                                    CTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCC                                                <  2:4106632/100‑1                                                                                                   AGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGC                 <  2:1365823/100‑1                                                                                                   AGAAAGGAAACGACAGGTGCTGAAAACGAGCTTTTGGCCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAG                  >  1:3584253/1‑99                                                                                                      AAGGAAACGAGAGGTGATGAAAACGAGCTTTTGGGCCTCTGTCGTTTCTTTTCTCTGTTTTTGACGGTGGAATTAACAATAGAAGTCAACAAAAAGCAG               >  1:742964/1‑99                                                                                                       AGGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCT             >  2:4012075/1‑100                                                                                                        GGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTG            >  2:2572800/1‑100                                                                                                        GGAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTG            <  2:4170988/100‑1                                                                                                         GAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGG           >  1:556888/1‑100                                                                                                         GAAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGG           >  1:881276/1‑100                                                                                                          AAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTTTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATAAAAGTAAACAACAAGTAGCTGGC          <  1:2241395/100‑1                                                                                                          AAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGC          <  1:4012055/100‑1                                                                                                          AAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGC          <  2:2192118/100‑1                                                                                                          AAACGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAAAAAAAAAAAAAAAAAAGCAGCTGGC          <  1:1741969/100‑1                                                                                                             CGACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGA       >  2:379601/1‑100                                                                                                              GACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGAC      <  2:3798011/100‑1                                                                                                              GACAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGAC      <  2:4034321/100‑1                                                                                                                CAGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTTGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACAT    >  1:1653046/1‑100                                                                                                                 AGGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATT   <  2:1456545/100‑1                                                                                                                  GGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTT  >  2:1574631/1‑100                                                                                                                                                                                                                       TGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTTGTTGACTTCCATTGTTCATTCCACGGCCAAAAACAGAGAAAGGAAACGACAG‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1636294‑1636407 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑agaaaggaaacgacagGTGCTGAAAACGAGCTTTTGGGCCTCTGTCGTTTCCTTTCTCTGTTTTTGGCCGTGGAATGAACAATGGAAGTCAACAAAAAGCAGCTGGCTGACATTT  <  NC_000913/1636432‑1636334

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.