New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_tpiA	= 2768828	20 (0.800)	4 (0.170)	4/274	2.9	15.6%	noncoding (12872/22030 nt)	cryptic prophage CP4‑57	cryptic prophage CP4‑57
	?	NC_000913_3_vch_tpiA	= 2768848	24 (1.010)					noncoding (12892/22030 nt)	cryptic prophage CP4‑57	cryptic prophage CP4‑57
Rejected: Frequency below/above cutoff threshold.

TCTTATTCGCCGTGACCGTCCGTTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACC  >  NC_000913_3_vch_tpiA/2768700‑2768994                                                                                                                                                     |                                                                                                                                                   tCTTATTCCCCGTTACCGTCCGTTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCt                                                                                                                                                    <  2:303057/149‑1 (MQ=255)   tcgttcgcCGTGACCGTCCGTTAACCCGTTATGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCAGCTGGACAGCCTGCAGCGGGAAGGCTtc                                                                                                                                                  <  2:185179‑M2/146‑3 (MQ=255)      gtcGCCGTGACCGTCCGTTATCCCGTGTAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGATTCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTtccag                                                                                                                                               >  2:7549‑M2/2‑144 (MQ=255)               aCCTTCCGTTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCttt                                                                                                                                      <  2:3121/149‑1 (MQ=255)                    ccgtTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTg                                                                                                                                 >  2:57444/1‑149 (MQ=255)                                      ttATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGa                                                                                                               <  1:255641/149‑1 (MQ=255)                                         tttCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGAccc                                                                                                            <  1:57444/149‑1 (MQ=255)                                              cgTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCCCAGCCACCGCTACACGTATATACCCACGATTTCCCTGCTGGACACCCTGCAGCGGGAGAGCTTCCAACCGTTCTTTGCCTCTCAGACACGGGTACGTAccccccccc                                                                                                       >  2:64565/1‑146 (MQ=255)                                                     cccAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGa                                                                                                <  1:324726/149‑1 (MQ=255)                                                          cGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATa                                                                                           >  2:377592/1‑149 (MQ=255)                                                                  gTGGGGATAAACCCGAATCCCGCAGGGCACGCTACACGTACATACCCACGATGCCCCTGCGGGACAGCCTCCAGCGGGAAGGCTGTCAGCCATTCTATGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCat                                                                                   <  2:412760/149‑1 (MQ=255)                                                                     aGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCTACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATAtg                                                                                <  2:207024/149‑1 (MQ=255)                                                                                gAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACg                                                                     >  1:332494/1‑149 (MQ=255)                                                                                      cGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTCCGTGACCCCCGCCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCgggg                                                               >  1:73517/1‑148 (MQ=255)                                                                                      cGCACTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTAGCCCGTCAGACACGCGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGa                                                               <  1:233698/149‑1 (MQ=255)                                                                                           tGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTACGCCTACGTCGGGAgggga                                                          >  1:280316/1‑148 (MQ=255)                                                                                                  tACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAACGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGCGCATACTAAGCATATGCTCCGCCTCCCTCGGGACGCGCaactgac                                                   >  2:155151/1‑144 (MQ=21)                                                                                                   acacGTGTCTACGCACTATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCCGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTTGTCGTGAGCATATTAAGCATATGCTTCGCCTACGTGGGGGGGGGCAGATTAcc                                                  <  2:36435/149‑1 (MQ=255)                                                                                                    cacGTATAGACCCAGTATTGCCGTTTTGGACAGTCTGCCGCGGGAAGGCTTTCAGCCATTCTTTGCCTGTCAGACACGGTTACGTGCACCCCGGCGTTTTGAGCATACTAATCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCg                                                 <  2:159617/149‑1 (MQ=21)                                                                                                                           tgctgGAGAGCCCGGAGCGGAAATGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCTGTCGTCGTGAGCATACTAAGCATATGTTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATc                          <  2:88940/149‑1 (MQ=21)                                                                                                                           tgctgGACAGCCTGCAGCGGGAAGGCTtccagcagggaaattgtgggtatatacgtgtagcgttcactgcg                                                                                                        <  2:7067‑M2/71‑45 (MQ=255)                                                                                                                           tgctgGACAGCCTGCAGCGGGAAGGCTtccagcagggaaattgtgggtatagacgtgtagcgttcactgcg                                                                                                        >  1:7067‑M2/1‑27 (MQ=255)                                                                                                                           tgctgGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGAGCAAATTACCGGTAAACAGGTTCAGGAAATTATc                          >  1:351156/1‑149 (MQ=255)                                                                                                                                  cAGCCTGCAGCGGGAAGGCTgtccagcagggaaattgtgggtatatacgtgtagcgttcactgcgggattcgtgtttatcctcactgaata                                                                             <  2:195812‑M2/91‑72 (MQ=255)                                                                                                                                  cAGCCTGCAGCGGGAAGGCTgtccagcagggaaattgtgggtatatacgtgtagcgttcactgcgggattcgtgtttatcctcactgaata                                                                             >  1:195812‑M2/1‑20 (MQ=255)                                                                                                                                      cTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTCCCGATAAACAGGTTCCGGACATTATCCTGCTTAActc               >  2:31881/1‑149 (MQ=255)                                                                                                                                                  ggCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCAt                                                                                            <  2:173088/60‑1 (MQ=255)                                                                                                                                                  ggCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCAt                                                                                            >  1:173088/1‑60 (MQ=255)                                                                                                                                                   gCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCAcc  >  2:48060/1‑149 (MQ=255)                                                                                                                                                     ttCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCgg                                                <  1:131329/101‑1 (MQ=255)                                                                                                                                                     ttCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCgg                                                >  2:131329/1‑101 (MQ=255)                                                                                                                                                     |                                                                                                                                                   TCTTATTCGCCGTGACCGTCCGTTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCTTAACTCTCACGATGGCACC  >  NC_000913_3_vch_tpiA/2768700‑2768994

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ 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.