New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	2291329 =	23 (1.250)	3 (0.170)	3/270	2.3	12.6%	noncoding (177/199 nt)	RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site	RIP160 (repetitive extragenic palindromic) element; contains 4 REP sequences and 1 IHF site
	?	NC_000913_3_vch_pgi	2291352 =	20 (1.160)					intergenic (+205/+6)	narP/ccmH	response regulator in two‑component regulatory system with NarQ/heme lyase, CcmH subunit
Rejected: Frequency below/above cutoff threshold.

ATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAAGAGTTTCAACATCATCTCCCACGCG  >  NC_000913_3_vch_pgi/2291184‑2291469                                                                                                                                                   |                                                                                                                                             agcagcagtgatttggcgaagccggtgccgcgtgggagatgatgttgaaactcttacctgccaacgatactcgcggtgcggtgattgaacgtagtatcgcgcaggcgatgcaacatttgtcgccgcaggagagtaaataaaaagagGcc                                                                                                                                            >  1:286834‑M1/147‑149 (MQ=255)    aCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGAt                                                                                                                                        <  1:62620/149‑1 (MQ=255)    aCAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCAT‑CGATGATCGGAAGAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGAt                                                                                                                                        >  1:239157/1‑149 (MQ=18)    aCAAACGCAAAACTGCCTGATGCGCTACGCGTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGAt                                                                                                                                        >  2:199135/1‑149 (MQ=255)      cagcgatttggcgaggccgttgccgcgtgggagatgatgtggaaactcttacctgccaacgatactcgccgtgcggtgattgaacgtagtatcgcgcaggcgatgcaacatttgtcgccgcaggagagtaaataaaaagagGCCCGATg                                                                                                                                       >  2:112758‑M1/142‑149 (MQ=255)      cagcgatttggcgaagccgttgccgcgtgggagatgatgttgaaactcttacctgccaacgatactcgccgtgcggtgattgaacgtagtatcgcgcaggcgatgcaacatttgtcgccgcaggagagtaaataaaaagagGCCCGATg                                                                                                                                       >  2:32976‑M1/142‑149 (MQ=255)                    cTGATGCGCTACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGAGGGCATGACCATCggcc                                                                                                                        >  1:281934/1‑147 (MQ=255)                     gccgttgccgcgtgggagatgatgttgaatctcttacctgccaacgatactcgccgtgcggtgattgaacgtagtatcgcgcaggcgatgcaacatttgtcgccgcaggagagtaaataaaaagagGCCCGATGGCATCACCATCGGGc                                                                                                                        >  1:174717‑M1/127‑149 (MQ=255)                      gATGCGCTACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCct                                                                                                                      >  1:122218/1‑149 (MQ=255)                       aTGCGCTACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCctc                                                                                                                     <  1:87006/149‑1 (MQ=255)                           gcTACGCTTATCAGGCCTACGTGGATG‑CCTCTGCCAAGTGGATTTACACAATTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCCACATCGGCCCTCtttt                                                                                                                 >  2:232408/1‑149 (MQ=18)                             tACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTttta                                                                                                               <  1:297539/149‑1 (MQ=255)                                           cTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTgcg                                                                                                 <  2:29648/149‑1 (MQ=255)                                             aCGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACGTTGTCAACAGTCGATCGCGATGGCATCACCAGCGGGCCTCTTTTTATGTACTCTCGTggggc                                                                                               >  1:43691/1‑149 (MQ=25)                                                    tcttacctgccaacgatactcgccgtgcggtgattgaacgtagtatcgcgcaggcgatgcaacatttgtcgccgcaggagagtaaataaaaagagGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTgcggc                                                                                               <  2:47218‑M1/48‑1 (MQ=255)                                                    tcttacctgccaacgatactcgccgtgcggtgattgaacgtagtatcgcgcaggcgatgcaacatttgtcgccgcaggagagtaaataaaaagagGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTgcggc                                                                                               >  1:47218‑M1/96‑143 (MQ=255)                                                        ataaaTTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGtt                                                                                     >  2:84649/4‑149 (MQ=255)                                                               tATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGc                                                                              <  1:97265/149‑1 (MQ=255)                                                                         acacAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGAta                                                                    <  2:122218/149‑1 (MQ=255)                                                                                    tAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCACGATGGCATCACCCTTGGGCATCTTTTTATTTACTCTCTTCCGGGTACAAATGTTGCATCGCCGGCGCGATACTACGTTCAAt                                                         >  2:190030/1‑149 (MQ=37)                                                                                       gCCGGATAGGGCGTTCACGCCGCATCCGCCATAAACGAAGCGCACTTTGTCAACAGTCTAGCACGATGGGATCGCCATCGGGCTTCGTTTTATTTAATTCCCTCCGGCGCCAACTGTTGCATCGCCTGCGCGATATTCCGTTCCATCAc                                                      >  2:75265/1‑149 (MQ=255)                                                                                       gCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTATTTTTATGTACTCTCCTGCGGCGACAAACGTTGCTTCGCCTGCGCGATACTACGTTCAATCAc                                                      >  1:288465/1‑149 (MQ=255)                                                                                                          cggcATCCTGCATAAACTAAGCGCACTGTGCCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTg                                   <  1:100015/147‑1 (MQ=255)                                                                                                               tCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAgg                              <  1:125249/149‑1 (MQ=255)                                                                                                                    cATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAaga                         <  1:106298/149‑1 (MQ=255)                                                                                                                         aCTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAAGAGTTTc                    <  1:190030/149‑1 (MQ=255)                                                                                                                              gcgcACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAAGAGTTTCAAcat               >  1:49175/1‑149 (MQ=255)                                                                                                                                 cACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAAGAGTTTCAAcatcat            >  2:121856/1‑149 (MQ=255)                                                                                                                                           aCAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAAGAGTTTCAACATCATCTCCCAcgcg  >  1:162354/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                             ATGACAAACGCAAAACTGCCTGATGCGCTACGCTTATCAGGCCTACGTGGATC‑GATCAATTTATTGAATTTACACAATTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATAAACTAAGCGCACTTTGTCAACAGTCTAGCCCGATGGCATCACCATCGGGCCTCTTTTTATTTACTCTCCTGCGGCGACAAATGTTGCATCGCCTGCGCGATACTACGTTCAATCACCGCACGGCGAGTATCGTTGGCAGGTAAGAGTTTCAACATCATCTCCCACGCG  >  NC_000913_3_vch_pgi/2291184‑2291469

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.