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.

CAAATCTTATTCGCCGTGACCGTCCGTTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCT  >  NC_000913_3_vch_tpiA/2768696‑2768975                                                                                                                                     |                                                                                                                                                    cAAATCTTATTCGCCGTGACCGTCCGTTAACCCGTGAAGCGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCCGGAAAGGCTGCAGCGGGaa                                                                                                                                     <  2:162454/149‑1 (MQ=255)     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)                                                                tATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGAcagccttcccgctgcaggctg                                                                                                                                >  1:195812‑M1/1‑70 (MQ=255)                                                                tATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGAcagccttcccgctgcaggctg                                                                                                                                <  2:195812‑M1/91‑22 (MQ=255)                                                                      gTGGGGATAAACCCGAATCCCGCAGGGCACGCTACACGTACATACCCACGATGCCCCTGCGGGACAGCCTCCAGCGGGAAGGCTGTCAGCCATTCTATGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCat                                                                <  2:412760/149‑1 (MQ=255)                                                                         aGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCTACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATAtg                                                             <  2:207024/149‑1 (MQ=255)                                                                                    gAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACg                                                  >  1:332494/1‑149 (MQ=255)                                                                                          cGCAGTGAACGCTACACGTCTATACCCACAATTTCCCTGCTGGAagccttcccgctgcaggctgtccagca                                                                                                                          >  1:7067‑M1/1‑44 (MQ=255)                                                                                          cGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGAagccttcccgctgcaggctgtccagca                                                                                                                          <  2:7067‑M1/71‑28 (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)                                                                                                                                 ctgGAagccttcccgctgcaggctgtccagcagggaaattgtgggtatatacgtgtagcgttcactgcgggaatcgtgtttatcctcactgaatacgctgggcaccacgcgaaataactctacacgggataacggacggtcacggcgac     >  2:7549‑M1/1‑5 (MQ=255)                                                                                                                                    gAagccttcccgctgcaggctgtccagctgggaaattgtgggtatatacgtgtagcgttcactgcgggattcgtgtttatcctcactgaatacgctgggcaccacgcgaaataactcataacgggttaacggacggtcacggcgaacga  <  2:185179‑M1/149‑148 (MQ=255)                                                                                                                                     |                                                                                                                                                    CAAATCTTATTCGCCGTGACCGTCCGTTAACCCGTGAAGAGTTATTTCGCGTGGTGCCCAGCGTATTCAGTGAGGATAAACACGAATCCCGCAGTGAACGCTACACGTATATACCCACAATTTCCCTGCTGGACAGCCTGCAGCGGGAAGGCTTCCAGCCATTCTTTGCCTGTCAGACACGGGTACGTGACCCCCGTCGTCGTGAGCATACTAAGCATATGCTGCGCCTACGTCGGGAGGGGCAAATTACCGGTAAACAGGTTCCGGAAATTATCCTGCT  >  NC_000913_3_vch_tpiA/2768696‑2768975

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.