New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_vch_pgi	3042303 =	NA (NA)	3 (0.170)	3/268	2.4	NA	intergenic (+10/+186)	ygfZ/yqfA	iron‑sulfur cluster repair protein, plumbagin resistance/hemolysin III family HylIII inner membrane protein
	?	NC_000913_3_vch_pgi	3042332 =	NA (NA)					noncoding (12/155 nt)	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences	REP210 (repetitive extragenic palindromic) element; contains 3 REP sequences

GATATGGAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAAA  >  NC_000913_3_vch_pgi/3042207‑3042478                                                                                                                              |                                                                                                                                                   gATATGGAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGCTGCGACCCTGGCGCGCCTCATCATGTCTg                                                                                                                             >  2:170097/1‑149 (MQ=255) gATATGGAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTg                                                                                                                             <  1:16142/149‑1 (MQ=255)      ggAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGAATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCAGGGCGGTCTTATCATGTCTGGGAtt                                                                                                                        >  1:306885/1‑149 (MQ=255)       gAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGAttt                                                                                                                       >  2:59282/1‑149 (MQ=255)       gAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAACCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGAttt                                                                                                                       <  1:28537/149‑1 (MQ=255)         aCCGGATAGCCTCGTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGa                                                                                                                     <  1:34916/149‑1 (MQ=255)          ccGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGGCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGGCTTATCATGTCTGGGATTTGAt                                                                                                                    >  2:81506/1‑149 (MQ=255)          ccGGAACGCATCTCCCCCGTAAGCGACGATGCGCATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGAt                                                                                                                    <  1:93035/149‑1 (MQ=39)                  cATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTg                                                                                                                             >  2:46947/1‑132 (MQ=255)                  cATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTg                                                                                                                             <  1:46947/132‑1 (MQ=255)                        ccGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCacaac                                                                                                      >  1:76226/1‑149 (MQ=255)                                gcgACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACACCAGAGAcca                                                                                              >  1:262961/1‑147 (MQ=255)                                     gaTGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTGTCACAACACGGACGAGGcaa                                                                                         >  2:320457/1‑147 (MQ=255)                                          gAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGAAGAGGCAAGTAGa                                                                                    >  1:4164/1‑149 (MQ=255)                                             tACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGGTCg                                                                                 <  2:184508/149‑1 (MQ=255)                                               cATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGa                                                                               <  2:76226/149‑1 (MQ=255)                                                  tgccgatCGGGCCGCTGCCGTAGTCGCTCGAAGAGGAAATCGCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTAACATGTCTGGGATTTGACGCCGTTATCACAACAGGGACGAGGCCCGTAGATCGGATaa                                                                            <  1:166729/144‑1 (MQ=255)                                                                   ctgttgtCGCTCCAAGAGCAAATCTCTTTATCGCATCAGGCATTGAGCGCCTGATGCGTCGCTGGCGCGTCTTATCCGGTCTGGGATTTGCTGCCTTTATCACAACAGTGACGACGCCCGTAGATCGGATAAGGCGTTCACGCCGAATc                                                           <  2:138059/143‑1 (MQ=255)                                                                   ccGTATTCGCCCGAAGAGTAAATCTCCTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATc                                                           <  1:23747/149‑1 (MQ=255)                                                                   ccGTACTCGTTCGAAGAGTAACTCTCTTTATCGCACCAGGAATTTAGCGCCGGATGCGACGCTGGCGCGTCTTATCATGTCTTGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATc                                                           <  2:138068/149‑1 (MQ=255)                                                                     gTATTCGCTGGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCg                                                         <  2:183760/149‑1 (MQ=255)                                                                           gCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGtt                                                   >  2:69790/1‑149 (MQ=255)                                                                            cTCGAAGAGAAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTtg                                                  <  1:176377/149‑1 (MQ=255)                                                                                aaGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGCGGCCCGTAGATCGGATAAGGCGTTCACGCCGAGTCCGGCAGTTGTGCt                                              >  2:179437/1‑149 (MQ=255)                                                                                  gagTAAATTTCTTTATCGCATCAGGCATTGATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTcc                                            <  1:321146/149‑1 (MQ=255)                                                                                     tAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGACGCACATCTCCTGCGAGACGCGAGGCAAGCATTGTGTATAAGGCGTTCACGCCGACTCGGTCAGTTGTGCTCCGAt                                         <  2:327422/149‑1 (MQ=16)                                                                                       aaTCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGAAGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGAACGGATACGGCGTTCACACCGAATCCGGAAGTTATGCTCCGATGc                                       >  2:269862/1‑149 (MQ=255)                                                                                                 TCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGCCAGTTGTGCTCCGATGCCTGATGCGAc                             <  1:41977‑M1/149‑1 (MQ=255)                                                                                                    CATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCt                          <  1:18600‑M1/149‑1 (MQ=255)                                                                                                     atcaggcgataaatgcctgatgcgaCGCTGGCGCGTCTTATCATGTCTGGGCTTTGATGCCTTGATAACAACAAGGACGAGGCCCGTAGAACGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGCAGCTg                         >  1:99889‑M2/26‑149 (MQ=255)                                                                                                        aggcgataaatgcctgatgcgaCGCTGGCGCGTCTTATCATGTCTg                                                                                                                             >  1:114687‑M2/23‑46 (MQ=255)                                                                                                        aggcgataaatgcctgatgcgaCGCTGGCGCGTCTTATCATGTCTg                                                                                                                             <  2:114687‑M2/24‑1 (MQ=255)                                                                                                            aTTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCGCGTc                  <  1:30505/149‑1 (MQ=255)                                                                                                             tttATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCGCGTCt                 <  2:288764/149‑1 (MQ=255)                                                                                                                aTCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCGCGTCTTAt              <  1:59282/149‑1 (MQ=255)                                                                                                                            gaCGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCa                                                      >  2:267399‑M2/3‑97 (MQ=255)                                                                                                                            gaCGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCa                                                      <  1:267399‑M2/95‑1 (MQ=255)                                                                                                                            gaCGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACaaa  >  1:171897‑M2/3‑149 (MQ=255)                                                                                                                            gaCGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCCCGGCTTATCAGGCCTACaaa  >  2:315675‑M2/3‑149 (MQ=255)                                                                                                                            gaCGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCAGGCGCGTCTTATCAGGCCTACaaa  >  1:114170‑M2/3‑149 (MQ=255)                                                                                                                              |                                                                                                                                                   GATATGGAACCGGATAGCATCTTCCGCGTACGCGACGATGCGAATACATTGCATATCGAGCCGCTGCCGTATTCGCTCGAAGAGTAAATCTCTTTATCGCATCAGGCATTTATCGCCTGATGCGACGCTGGCGCGTCTTATCATGTCTGGGATTTGATGCCTTTATCACAACAGGGACGAGGCCCGTAGATCGGATAAGGCGTTCACGCCGAATCCGGCAGTTGTGCTCCGATGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTACAAA  >  NC_000913_3_vch_pgi/3042207‑3042478

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