New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_pae_tpiA	= 3682074	46 (1.370)	5 (0.160)	5/266	3.6	10.0%	intergenic (‑134/+87)	yhjJ/dctA	putative periplasmic M16 family chaperone/C4‑dicarboxylic acid, orotate and citrate transporter
	?	NC_000913_3_pae_tpiA	= 3682087	47 (1.480)					intergenic (‑147/+74)	yhjJ/dctA	putative periplasmic M16 family chaperone/C4‑dicarboxylic acid, orotate and citrate transporter
Rejected: Coverage evenness skew score above cutoff.
Rejected: Frequency below/above cutoff threshold.

GAACCCCTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGTTTTTTGTGGTCCAGT  >  NC_000913_3_pae_tpiA/3681943‑3682236                                                                                                                                                  |                                                                                                                                                      gAACCCCTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTc                                                                                                                                                  <  2:161300/150‑1 (MQ=255)   aCCCCTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAg                                                                                                                                                >  2:382803/1‑150 (MQ=255)    ccccTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAgg                                                                                                                                               <  1:277942/150‑1 (MQ=255)     cccTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGc                                                                                                                                              >  2:297545/1‑150 (MQ=255)     cccTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAAAGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACAGGAAAATGTCACGGGCGA‑AGTGCAATAACCCTGGACTCACGCAGGTGGGAGGTTTAgcc                                                                                                                                              >  1:57636/1‑148 (MQ=255)           ccAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAACACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAggg                                                                                                                                        <  1:24706/149‑1 (MQ=255)                tATCCTGGGAATAAAAAAACTGCCCGTTGTCGGTCAGTCACAATGGCGTTAAAAACACTACGGGTTAGACCGCAAGAACATGAAAATGTCACGGAGGA‑ACGGACGACAACCTGAACTCACAAAGGCGGTAGCATCAGCCACAgggctaac                                                                                                                                   >  2:348357/1‑145 (MQ=255)                    cTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAAt                                                                                                                                  >  2:580643/1‑147 (MQ=255)                    cTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAAt                                                                                                                                  <  1:580643/147‑1 (MQ=255)                    cTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTAt                                                                                                                               >  1:352530/1‑150 (MQ=255)                    cTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGGCAATGAt                                                                                                                               >  1:352132/1‑150 (MQ=255)                     tGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATg                                                                                                                              >  1:449627/1‑150 (MQ=255)                      ggTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATgc                                                                                                                             >  1:546877/1‑150 (MQ=255)                         aataaAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGAGAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAAATCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCa                                                                                                                          >  2:503991/1‑150 (MQ=255)                                             tCGGTCAGTCTAAATGAGGTTAGGAACACTTCGTGTTACCCAGCAAGAACATAAAAAAG‑ATCGGAAGAGAGTGGTGTAGACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGAGAAg                                                                                                      >  2:127648/1‑150 (MQ=255)                                                     tCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCTGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCg                                                                                              >  1:527815/1‑150 (MQ=255)                                                     tCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGAAGTGCg                                                                                              >  1:104507/1‑150 (MQ=255)                                                      ttAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCgg                                                                                             <  2:439675/149‑1 (MQ=255)                                                      cTAAATGACGTTAAAAAGACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCgg                                                                                             <  2:94569/150‑1 (MQ=255)                                                       tAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCggg                                                                                            >  1:310093/1‑150 (MQ=255)                                                       aaaaTTACGTTAAAAACATTGCGGGATAGACCGCAAGAACATGAAAATGTGACGGAAGA‑AGTGAAATAAACCTGAACACACCCAGGTGGTAAGTTCAGGCACCGGACGCAAGTATGCGCAAACATCCGCACTCGGGGAAGGGAGTGCtgg                                                                                            <  2:522368/149‑1 (MQ=255)                                                                ttAAAAACGCTTCGGGTTAGACCGCAAGAACATGAAAATGTCACCGAAGA‑AGTGAAATAAATCTGAACTCACCCAGGTGGTAAGTTCAGGCAGAGGGGTCAATTATGCGCAAACTCCCGCACTCGGGGAAGGGAGTGCGGTCATAAGtga                                                                                   <  2:138988/150‑1 (MQ=255)                                                                ttAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAATGCGGGCATAAGtga                                                                                   >  1:419836/1‑150 (MQ=255)                                                                      acacTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGAt                                                                             <  2:292584/150‑1 (MQ=255)                                                                       cacTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGAtt                                                                            <  1:378480/150‑1 (MQ=255)                                                                          ttCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGTGGTAAATTATGCGCAAACACCCGCACTCGTGGAGGGGAGTGCGGGCATCAGTGGTGAGATTaaa                                                                         >  2:278076/1‑149 (MQ=255)                                                                          ttCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAACCACCCGCACTCGGGGAAGGGAGTGGGGGACTAAGTGATGAGATTaaa                                                                         >  1:368658/1‑149 (MQ=255)                                                                                ttAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGAt                                                                    <  2:4554/149‑1 (MQ=255)                                                                                ttAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGAt                                                                    >  1:4554/1‑149 (MQ=255)                                                                                   gACCGCAAGAACATGAAAAGGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGGGGTAAGTTCAGGCACAGGGGTCAATAATACGCAAACACCCGCACTCGGGGAAGGGAAGACGGGCATAAGTGATGAGATTAAGAGGATAAtt                                                                >  1:533451/1‑150 (MQ=255)                                                                                      cGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGATGGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGt                                                             <  2:546877/150‑1 (MQ=255)                                                                                       gCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTg                                                            <  1:157906/150‑1 (MQ=255)                                                                                           gAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGtt                                                        <  1:50247/150‑1 (MQ=255)                                                                                             aCATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGtttt                                                      <  2:436710/150‑1 (MQ=255)                                                                                               aTGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAGACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGttttca                                                    >  2:173019/1‑148 (MQ=255)                                                                                                        tCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGgcg                                           >  1:173176/1‑150 (MQ=255)                                                                                                          aCGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACACGGGTCAATTAGGCGCAAACACCCGCACTCGGGGAAGGGAGGGCGGGCATAAGTGATGAGAGTAAGAGGATAATTCGTGCGTTTTTCCATCcgccgcc                                         >  1:294226/1‑149 (MQ=255)                                                                                                             gaaga‑aGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGCGCGCAACAGGTTAATTCGTGCGTTTTGCCATCCGGCGCACgc                                      >  1:316255/1‑149 (MQ=255)                                                                                                                ga‑agGGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCAGTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCTCACgtgtt                                   <  2:284797/150‑5 (MQ=255)                                                                                                                        aaTAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGca                            <  2:564628/150‑1 (MQ=255)                                                                                                                               cTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGAAAACACCCGCACTCGGGGAAGGGAGTACGGGCATAAGTGATGAGATTAAGAGGATAATTCGTACGTTTTGCTATCCAGCGCAAGATTATTCAGCACATCGTc                     >  2:462099/1‑150 (MQ=255)                                                                                                                                tGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTcc                    <  2:36845/150‑1 (MQ=255)                                                                                                                                        cccAGGTGGTAAGTTCAGGCACAGGGGTTAATTATGCGCAAACACGCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGtttttt            <  2:294226/150‑1 (MQ=255)                                                                                                                                        cccAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGtttttt            <  2:101806/150‑1 (MQ=255)                                                                                                                                         ccAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGTTTTTtg           >  1:472717/1‑150 (MQ=255)                                                                                                                                          cAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATaa                                                                  >  2:520506/1‑94 (MQ=255)                                                                                                                                          cAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATaa                                                                  <  1:520506/94‑1 (MQ=255)                                                                                                                                             gtggtAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGTTTTTTGTGGt       <  1:297545/150‑1 (MQ=255)                                                                                                                                              gggtAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGTGTTTGGTTTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGTTTTTTGTGGTc      <  2:449627/149‑1 (MQ=255)                                                                                                                                                gtAAGTTCAGGCAAAGGGGTCAATTATGGGCAACCACCCGCACTCAGGGCAGCGAGTCCTCGCATAAGTGACGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTAGTTAGCACATCGTCCAGTGTTTTGTGGTCCa    <  2:65058/150‑1 (MQ=255)                                                                                                                                                  aaGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAATGCGGGCGTAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGTTTTTTGTGGTCCAGt  >  1:321481/1‑150 (MQ=255)                                                                                                                                                  |                                                                                                                                                      GAACCCCTGATCAACTATCCTGGTAATAAAAAAACTGCCCGTTGTCGGTCAGTCTAAATGACGTTAAAAACACTTCGTGTTAGACCGCAAGAACATGAAAATGTCACGGAAGA‑AGTGAAATAAACCTGAACTCACCCAGGTGGTAAGTTCAGGCACAGGGGTCAATTATGCGCAAACACCCGCACTCGGGGAAGGGAGTGCGGGCATAAGTGATGAGATTAAGAGGATAATTCGTGCGTTTTGCCATCCGGCGCACGATTATTCAGCACATCGTCCAGTTTTTTGTGGTCCAGT  >  NC_000913_3_pae_tpiA/3681943‑3682236

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.