New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 1207805	43 (1.120)	10 (0.290)	10/252	2.5	19.0%	noncoding (11586/15193 nt)	cryptic prophage e14	cryptic prophage e14
	?	NC_000913_3_vch_tpiA	= 1209602	47 (1.380)					noncoding (13383/15193 nt)	cryptic prophage e14	cryptic prophage e14
Rejected: Frequency below/above cutoff threshold.

TCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATG  >  NC_000913_3_vch_tpiA/1207660‑1207945                                                                                                                                                  |                                                                                                                                              tCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGc                                                                                                                                            >  1:357251/1‑149 (MQ=255)   cGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGATTGGGAGAAGCctctg                                                                                                                                          >  1:451199‑M1/1‑144 (MQ=255)     gTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCaaaa                                                                                                                                        <  1:432389/149‑1 (MQ=255)       gCCAGCCGGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcatt                                                                                                                                      <  1:313763‑M1/149‑10 (MQ=255)         cAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGCGAAGGAGCAAAAC‑TCa                                                                                                                                   >  2:499135/1‑149 (MQ=255)          aGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCaa                                                                                                                                  <  2:246656/149‑1 (MQ=255)              tGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCCAGAATCCGGTTGGCGATATCAAATCGGATGGCACTGTGCAAAAGGCTCTCGAAAACCTTGGTTTGGGAGCAGGctctgcgtttccggtt                                                                                                                               >  1:116379‑M1/1‑133 (MQ=255)               ggAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttg                                                                                                                              <  2:372016‑M1/149‑18 (MQ=255)               ggAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATgccg                                                                                                                             <  2:623191/149‑3 (MQ=255)                gagaAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATgcagc                                                                                                                            <  1:251705/149‑1 (MQ=255)                        gcggcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTa                                                                                                                    >  2:310927/1‑149 (MQ=255)                        gcggcACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGAGCAAACGTCTCTCGAAACTCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTa                                                                                                                    <  1:267709/149‑1 (MQ=255)                             ccGATCAGTTACGTACCCCACTTCGCGCGCTGCTGTTGAGCTGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTa                                                                                                               <  1:487187/148‑1 (MQ=25)                               gACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGCTGGCACTGTGCAAGCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAgg                                                                                                             >  2:540531/1‑149 (MQ=255)                               gACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCAGATAGCACTGTGCAAACGACTCTCGAAAACCTTGGTTTGGGCGACGGA‑CAAAACATCAATCACACAACGGCTAcctaaag                                                                                                             >  2:308583/1‑143 (MQ=17)                                     ttacttacCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCAc                                                                                                       >  2:631805/1‑149 (MQ=255)                                     ttacttacCGCACTTCCCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAAAGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCAc                                                                                                       <  1:129043/149‑1 (MQ=255)                                              gCACTTCGCGCGCTGCTGTTAAGCCGAAAGAATCCGGTTGGCGATATCAAAACGGATGGCACTGTGCAAACGGCTCTCTAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCAt                                                                                              <  2:637997/149‑1 (MQ=255)                                                aCTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAACTCGGCTGTTACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgc                                                                                             <  1:156271‑M1/149‑51 (MQ=255)                                                aCTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAg                                                                                            <  1:310927/149‑1 (MQ=255)                                                aCTGCGCGCGCTGCTGTTAAGCCGAAAGAAGCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTTTCGAAAACCTTGGTTTGGGAGAACGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAg                                                                                            <  1:193690/149‑1 (MQ=25)                                                  ttCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCt                                                                                          >  1:604783/1‑149 (MQ=255)                                                         gctgctGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggggtcccggttccgtggccttcagccactccgccaccaggct                                                                                    >  2:24190‑M1/1‑90 (MQ=255)                                                               gctctgCCGCAAGAGGCCGTTCGGAGAATACAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATGCCGGTTATGa                                                                             <  1:657503/144‑1 (MQ=37)                                                                ttAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaa                                                                             >  1:370757‑M1/1‑83 (MQ=255)                                                                 tAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCACAGCTATACCGGTTATGAtt                                                                           <  1:385792/149‑1 (MQ=255)                                                                     ccGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCTATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtggtg                                                                       <  1:398534/149‑1 (MQ=255)                                                                       gCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTc                                                                                                >  2:408414/1‑122 (MQ=255)                                                                       gCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTc                                                                                                <  1:408414/122‑1 (MQ=255)                                                                                cGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCaa                                                            <  2:591309/149‑1 (MQ=255)                                                                                      gCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATgca                                                                                                                              <  1:642918/77‑1 (MQ=255)                                                                                      gCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATgca                                                                                                                              >  2:642918/1‑77 (MQ=255)                                                                                        gatactaaatcggatGTCACGGTCCAAATGGCTTTCGAAACGCTGGGTTTGGGAGAAGGctctgcattacctgttggtggcccggttccgtggccttcagccactcctccaacaggctggctgaaatgcaatggtgccgctttttctgc                                                     <  2:259287‑M1/143‑91 (MQ=255)                                                                                        gATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATCCCGGTTAGGATTGGTGGGATTGAGCCATAAGTAAt                                                    >  2:31153/1‑149 (MQ=38)                                                                                                  cGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtgg                                                                         <  1:284780/118‑1 (MQ=255)                                                                                                  cGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtgg                                                                         >  2:284780/1‑118 (MQ=255)                                                                                                  cGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTgg                                          <  1:631805/149‑1 (MQ=255)                                                                                                     aTGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttttctgctgaagaatacccg                                        >  2:202415‑M1/1‑46 (MQ=255)                                                                                                     aTGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGAAGCAACGGCTACATTAGCACTCACCTGTTTCATAGCTATACCGGGTATGATTGGTAGTATTGAGCAATCAGTAATCATTCAGTggggg                                       >  1:159427/1‑149 (MQ=39)                                                                                                      tGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGt                                      <  1:156097/149‑1 (MQ=255)                                                                                                              tgCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGATATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGcc                              <  2:633442/149‑1 (MQ=255)                                                                                                                 aaaCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATg                                                                                                                                <  2:140118/48‑1 (MQ=255)                                                                                                                 aaaCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATg                                                                                                                                >  1:140118/1‑48 (MQ=255)                                                                                                                       ctctCGAAAACCTTGGTTTGGGAGAAGGctctgcattacctgttagtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttttctgctgaagaatacccggaactggcaaaggcttat                      >  1:65505‑M1/1‑28 (MQ=255)                                                                                                                          tcGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCt                  >  1:672857/1‑149 (MQ=255)                                                                                                                          tcGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCt                  >  2:634012/1‑149 (MQ=255)                                                                                                                            gAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGc                <  2:604783/149‑1 (MQ=255)                                                                                                                               aaCGTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCctc             >  1:659574/1‑149 (MQ=255)                                                                                                                                 cgttGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTg           >  1:648801/3‑149 (MQ=255)                                                                                                                                  cTTGGGTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTAATAGCTATACCGGTTATGATTGGTGGTATTTAACAATCAGTAATCATTCACTGGGGGTGGCATACCGCGAAATCATCTGctcctgt          >  2:289346/1‑143 (MQ=255)                                                                                                                                   ttGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCCGTGGGACTGGAATGCCGCAAAAGCATCTGCCTCTggg         <  1:163338/149‑1 (MQ=255)                                                                                                                                   ttGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTggg         <  1:634012/149‑1 (MQ=255)                                                                                                                                        ttGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGa    <  2:478254/149‑1 (MQ=255)                                                                                                                                         tGGGAGAAGGctctgcattacctgtcggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcactggtgccgctttttctgctgtagaatacccggaactggcaaaggcttatccgacaaataaattgcct    <  1:607929‑M1/149‑140 (MQ=255)                                                                                                                                           ggAGAAGGctctgcattacctgttggtgtcccggttccgtggccttcagccactccgccaacaggctggctgaaatgcaatggtgccgctttttctgctgaagaatacccggaactggcaaaggcttatccgacaaataaattgcctga  <  2:667978‑M1/149‑142 (MQ=255)                                                                                                                                                  |                                                                                                                                              TCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGGGGGGATG  >  NC_000913_3_vch_tpiA/1207660‑1207945

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.