New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	1207790 =	38 (0.990)	7 (0.210)	7/252	3.4	14.8%	noncoding (11571/15193 nt)	cryptic prophage e14	cryptic prophage e14
	?	NC_000913_3_vch_tpiA	1209619 =	47 (1.380)					noncoding (13400/15193 nt)	cryptic prophage e14	cryptic prophage e14
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

TGCAGCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGG  >  NC_000913_3_vch_tpiA/1207642‑1207938                                                                                                                                                     |                                                                                                                                                      tGCAGCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCT                                                                                                                                                       >  2:620243‑M1/1‑149 (MQ=255)         ggtggAGGCACCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGG                                                                                                                                               <  1:542983‑M1/149‑1 (MQ=255)          gtggAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTTGCGTGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGG                                                                                                                                              >  1:633442‑M1/1‑149 (MQ=255)          gtggAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGG                                                                                                                                              <  1:37489‑M1/149‑1 (MQ=255)                   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                                                                                                                       >  2:642918/1‑77 (MQ=255)                                                                                                        gCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATgca                                                                                                                       <  1:642918/77‑1 (MQ=255)                                                                                                          gatactaaatcggatGTCACGGTCCAAATGGCTTTCGAAACGCTGGGTTTGGGAGAAGGctctgcattacctgttggtggcccggttccgtggccttcagccactcctccaacaggctggctgaaatgcaatggtgccgctttttctgc                                              <  2:259287‑M1/143‑91 (MQ=255)                                                                                                          gATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATCCCGGTTAGGATTGGTGGGATTGAGCCATAAGTAAt                                             >  2:31153/1‑149 (MQ=38)                                                                                                                    cGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtgg                                                                  >  2:284780/1‑118 (MQ=255)                                                                                                                    cGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATtgg                                                                  <  1:284780/118‑1 (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                                                                                                                         >  1:140118/1‑48 (MQ=255)                                                                                                                                   aaaCGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATg                                                                                                                         <  2:140118/48‑1 (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)                                                                                                                                                     |                                                                                                                                                      TGCAGCGTGGTGGAGGCATCCGGTGCCAGCCTGGAGAAGGGGCGGCACGACCAGTTACTTACCGCACTTCGCGCGCTGCTGTTAAGCCGCAAGAATCCGTTTGGCGATATCAAATCGGATGGCACTGTGCAAACGGCTCTCGAAAACCTTGGTTTGGGAGAAGGAGCAAAAC‑TCAATGCAGCAACGGCTACATTAGGACGCACCGGTTTCATAGCTATACCGGTTATGATTGGTGGTATTGAGCAATCAGTAATCATTCAGTGGGGGTGGAATGCCGCAAAAGCATCTGCCTCTGGG  >  NC_000913_3_vch_tpiA/1207642‑1207938

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.