New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_pgi	1097372 =	NA (NA)	9 (0.130)	9/272	7.1	14.3%	intergenic (+543/+193)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
	?	NC_000913_3_pae_pgi	1097531 =	55 (0.810)					intergenic (+702/+34)	ycdU/serX	putative inner membrane protein/tRNA‑Ser
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

ACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGA  >  NC_000913_3_pae_pgi/1097437‑1097677                                                                                               |                                                                                                                                                      aCTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCg                                                                                               >  2:962958/1‑149 (MQ=31)  cTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGa                                                                                              >  1:516530/1‑149 (MQ=32)   tGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTCTAAAAATGGCGGTGAGGGGGGGATTCGaa                                                                                             >  2:662886/1‑149 (MQ=17)       ttCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGCGCTCTTCTTTAAATATGGCGGTGCGGCGGGGATTCGcccccc                                                                                         >  2:553465/1‑149 (MQ=11)          aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAcc                                                                                           <  1:1109351/144‑1 (MQ=34)          aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAcc                                                                                           <  1:1110058/144‑1 (MQ=34)          aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAcc                                                                                           >  2:1110058/1‑144 (MQ=34)          aCGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAAcc                                                                                           >  2:1109351/1‑144 (MQ=34)             gTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAAAATGGCGGTGAGGGGGGGATTCGAACCCCCGATAc                                                                                   >  1:1086709/1‑149 (MQ=255)                  tCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGc                                                                              <  2:516530/149‑1 (MQ=255)                   ccAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGcc                                                                             <  1:390258/149‑1 (MQ=255)                     aaCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGGTACGTTGCCGt                                                                           >  1:974996/1‑149 (MQ=255)                     aaCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCgg                                                                           >  2:587674/1‑148 (MQ=255)                     aaCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGt                                                                           <  1:78637/149‑1 (MQ=255)                     aaCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGt                                                                           <  1:758023/149‑1 (MQ=255)                                gCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAAGTGGGGGTTCGAACCCCCGATACGTTGCCTTA‑TACACACttt                                                               >  1:834251/1‑149 (MQ=255)                                 ccAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGta‑ta                                                                       <  2:310352/140‑1 (MQ=255)                                 ccAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGta‑ta                                                                       >  1:310352/1‑140 (MQ=255)                                    gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGAAGCGAACCCCCGCTACGCGGCCGTAGTAC‑CACCTTCCAg                                                           >  1:582583/1‑149 (MQ=11)                                      tGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGc                                                         <  2:530621/149‑1 (MQ=255)                                       gTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TC‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCCTC‑TACACACTTTCCAGGCg                                                        >  2:895313/1‑149 (MQ=255)                                        tCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGc                                                                              >  2:1117234/1‑127 (MQ=255)                                        tCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGc                                                                              <  1:1117234/127‑1 (MQ=255)                                              cccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCt                                                 >  1:1099367/1‑149 (MQ=255)                                              cccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCt                                                 >  2:15371/1‑149 (MQ=255)                                               ccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCtt                                                >  1:569158/1‑149 (MQ=255)                                               ccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCtt                                                >  1:1110226/1‑149 (MQ=255)                                                   tCGCGGTTTCTTATCCCCCCGGTTTGTGCAATTTACGAAAAAAAAGCCCGTACTTTCG‑TA‑CTAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGc                                            <  2:157976/149‑1 (MQ=17)                                                     ggggCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCa                                          >  2:1119455/1‑149 (MQ=255)                                                           tctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGa                                    <  2:95886/149‑1 (MQ=255)                                                             tcATCCCCCCGGTGTGTGCAATAGACGAAAAACAA‑ACCGT‑CGTTCGCTACCGAGCTCTTCTTTAAATATGGCGGGGAGGGGGGGATTCGACCCCCCGATACGTTGCCGTA‑TAAAAACTTTCCAGGCTTGCCCCTTCACCCCCCCGGaca                                  >  2:815707/1‑149 (MQ=9)                                                                  ctcacGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTACTGTAACCCGGGCGGCGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCGCa                             <  2:133557/145‑1 (MQ=14)                                                                    cccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGta‑ta                                                                       <  1:180992/105‑1 (MQ=255)                                                                    cccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGta‑ta                                                                       >  2:180992/1‑105 (MQ=255)                                                                    cccGGGGTGTGCAATATACGAAAAAAAAGCCCGTACTGTCT‑TA‑CGAGCTCTTCTGTAAATAGGACGGGGAGGGGGGGATTAGAAGACCCGGTACATGTCCGTA‑TACGCACTTTCAAGTAATGCTCCCTACGCCACTAGGACACCTCagc                           >  2:16652/1‑147 (MQ=9)                                                                       tgtctgtgTAATACACGAAAAAAAAGCCCGTACCTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCaaa                        <  2:534191/145‑1 (MQ=255)                                                                         tgtgtgCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAAtt                      <  1:15371/149‑1 (MQ=255)                                                                            gtgCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTc                   <  2:1099367/149‑1 (MQ=255)                                                                            gtgCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGAGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTc                   <  2:970773/149‑1 (MQ=255)                                                                             tgCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCg                  >  2:974117/1‑149 (MQ=255)                                                                             tgCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCACTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCTAGTCATGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTca                  >  1:943310/1‑148 (MQ=255)                                                                              gCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAAACGTGCCCCTTCAGCCACTCGGACACCTCCCCAAATTGTCGt                 >  2:240427/1‑149 (MQ=255)                                                                                 atatACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACGTCACCAAATTGTCGTTcc              >  1:317054/1‑149 (MQ=255)                                                                                     aCGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTc          <  1:840109/149‑1 (MQ=255)                                                                                       gAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGTTCGGAGCATAGATACGTTGACGTC‑TACAAGCATACCAGGCGTCCTCCTTTAGCGACCCGGACACCCCACCAAATCGTCTTTCCTGTCtt        >  2:106540/1‑149 (MQ=14)                                                                                       gAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTc                                                                                                <  2:10932/62‑1 (MQ=31)                                                                                       gAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTc                                                                                                >  1:10932/1‑62 (MQ=31)                                                                                       gAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGt                    >  2:329687/1‑137 (MQ=37)                                                                                       gAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGt                    <  1:329687/137‑1 (MQ=34)                                                                                       gAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGAAACCTCACCAAATTGTAGTTCCTGTCtt        >  1:994733/1‑149 (MQ=255)                                                                                        aaaaaaaaGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTg       <  1:553465/149‑1 (MQ=255)                                                                                          aaaaaaGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCt     <  2:1143759/149‑1 (MQ=255)                                                                                            aaaaGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGcc                                                                             <  1:870624/76‑1 (MQ=40)                                                                                            aaaaGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGcc                                                                             >  2:870624/1‑76 (MQ=255)                                                                                             aaaGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGa  >  2:722942/1‑149 (MQ=255)                                                                                               |                                                                                                                                                      ACTGCGTTCACGGTCTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCG‑TA‑CGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTA‑TACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGA  >  NC_000913_3_pae_pgi/1097437‑1097677

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.