New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	= 4040683	50 (1.120)	13 (0.300)	7/274	4.7	21.6%	intergenic (+47/+223)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
	?	NC_000913_3_pae_pgi	= 4213162	45 (1.030)					intergenic (+3/‑72)	rrfE/yjaA	5S ribosomal RNA of rrnE operon/stress‑induced protein
Rejected: Coverage evenness skew score above cutoff.

AGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAGTGTCAG  >  NC_000913_3_pae_pgi/4213018‑4213309                                                                                                                                                 |                                                                                                                                                     aGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTa                                                                                                                                                  <  1:453932/149‑1 (MQ=31)  gCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAg                                                                                                                                                 <  1:145131/149‑1 (MQ=32)        tGATAAAACAGAAGTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAAc                                                                                                                                           <  2:678779/149‑1 (MQ=37)          aaaaaaCAGAATTGGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCATGCAGCAACTTCGAAAAAgcc                                                                                                                                         <  2:174435/147‑1 (MQ=11)           tAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAAcccc                                                                                                                                        >  1:27603/1‑149 (MQ=39)            aaaaCAGAATTTGCCTGGCGGCAGGAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCg                                                                                                                                       <  2:422726/149‑1 (MQ=255)              aaCAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGt                                                                                                                                     >  2:249229/1‑149 (MQ=255)                 aGAATCTGCCTGGGGGCAGTAGCGTGGTGGTCCCACCTGACCCCATGGCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCa                                                                                                                                  <  1:375234/149‑1 (MQ=255)                                     aGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCa                                                                                                             <  1:206281/149‑1 (MQ=255)                                         cgGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATc                                                                                                         <  2:769148/149‑1 (MQ=255)                                                cccACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAattatt                                                                                                  >  1:683848/1‑149 (MQ=255)                                                 ccACCTGACCCCATGCCGAACTAAGAAGTGAAACGCCGTAGCGACGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGAGAACTGCCCGGCATCAAATGAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATCTCAATTAttt                                                                                                 >  1:184866/1‑149 (MQ=18)                                                        aCCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCatgat                                                                                          <  2:6289/149‑1 (MQ=255)                                                          cccATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCCTACGG‑CCGGGGTTTTTTGCATATCAATTATTTGCAtgatga                                                                                        >  1:345881/1‑149 (MQ=255)                                                                     cTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGG‑CCTTATGGACCGGGGtttttcta                                                                                                              <  1:25894/116‑4 (MQ=14)                                                                     cTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGG‑CCTTATGGACCGGGGtttttcta                                                                                                              >  2:25894/1‑113 (MQ=14)                                                                      tCAGTAGTGAAAGGCCGTATCGCCTGTGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAACACCCTGGTCCATTGGG‑CCGGGGTTTTTTGCATATCAATTATTTGCTTGATGAAGGGAATCTCAt                                                                            <  2:29659/149‑1 (MQ=21)                                                                      tCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAAtctact                                                                            >  2:416336/1‑146 (MQ=255)                                                                           aGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAg                                                                       <  1:440808/149‑1 (MQ=255)                                                                                 aCGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGt                                                                 <  1:201766/149‑1 (MQ=255)                                                                                           gcCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAAt                                                       <  2:345881/149‑1 (MQ=255)                                                                                           gcCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGGTCTGTAAATCCaact                                                       >  2:79568/1‑147 (MQ=255)                                                                                           gcCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAAATGCTAAGCATCAAATTAGCACCCCTCCAGCCTATTATA‑ACGAAGTTCTTGCTATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAAt                                                       <  1:581721/149‑1 (MQ=16)                                                                                                tGGTAGTTGGGGGGCTCCCCGTGCGAGATGAGGGAACTGACAAGCATCAAATTAGAAATACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATtcgtc                                                  <  2:184866/149‑1 (MQ=255)                                                                                                tGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATtcgtc                                                  <  1:235434/149‑1 (MQ=255)                                                                                                tGGTAGTGTGGGGTCGCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATtcgtc                                                  <  1:667128/149‑1 (MQ=255)                                                                                                 ggTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATATCATGTCAGTTCTGTATATTCAAATtcgtcg                                                 <  2:683848/149‑1 (MQ=255)                                                                                                  gTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTcgtcgt                                                >  2:66034/1‑149 (MQ=255)                                                                                                           ggTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAAtt                                       >  2:542895/1‑149 (MQ=255)                                                                                                                 cccATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGtt                                 >  1:701439/1‑149 (MQ=255)                                                                                                                    aTGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCAAAATTCGTCGTAATCAAATTACTGTTctc                              >  2:671565/1‑147 (MQ=255)                                                                                                                        gagaGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATc                          <  2:699212/149‑1 (MQ=255)                                                                                                                             gaGGGAACGGCCAGGCAGCAAATTAGAAAAACCCCGTGCCATAAGG‑TCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGaa                     <  2:106406/148‑1 (MQ=255)                                                                                                                              aGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGaaa                    <  2:456875/149‑1 (MQ=255)                                                                                                                                  aaCTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCaa                >  2:136126/1‑149 (MQ=255)                                                                                                                                   aCTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCaaa               <  2:557839/149‑1 (MQ=255)                                                                                                                                    cTGCCAGGCATCAAATTAGAAAAACCCCGGTCCGTAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAAc              <  2:27603/149‑1 (MQ=255)                                                                                                                                    cTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAAc              <  1:66034/149‑1 (MQ=255)                                                                                                                                     tGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACg             >  2:552595/1‑149 (MQ=255)                                                                                                                                       ccAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCAt                                                                            >  2:249487/1‑84 (MQ=255)                                                                                                                                       ccAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCAt                                                                            <  1:249487/84‑1 (MQ=255)                                                                                                                                         aGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGaa         <  1:736679/149‑1 (MQ=255)                                                                                                                                           gCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAgt       <  1:136126/149‑1 (MQ=255)                                                                                                                                                aaaTTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAGTGTCAg  <  1:249229/149‑1 (MQ=255)                                                                                                                                                aaaTTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTCGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAGTGTCAg  <  2:644431/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                     AGCGGTCTGATAAAACAGAATTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAAACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGCATCAAATTAGAAAAACCCCGGTCCATAAGG‑CCGGGGTTTTTTGCATATCAATTATTTGCATGATGAAGGGAATCTCATGTCAGTTCTGTATATCCAAATTCGTCGTAATCAAATTACTGTTCGCGATCTTGAAAGCAAACGTGAAGTGTCAG  >  NC_000913_3_pae_pgi/4213018‑4213309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.