New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_tpiA	1596351 =	1 (0.020)	44 (0.910)	38/282	0.4	97.8%	pseudogene (1637/3861 nt)	yneO	pseudogene, AidA homolog
	?	NC_000913_3_hsa_tpiA	= 1651548	NA (NA)					intergenic (+11/‑3)	insD1/intQ	IS2 transposase TnpB;IS, phage, Tn; Transposon‑related functions; extrachromosomal; transposon related/pseudogene, Qin prophage; phage integrase family;Phage or Prophage Related

AGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGC  >  NC_000913_3_hsa_tpiA/1651416‑1651696                                                                                                                                     |                                                                                                                                                     agGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGctc                                                                                                                                      <  1:228854/149‑1 (MQ=255)   gCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGctcct                                                                                                                                    >  2:792302/1‑149 (MQ=255)       tCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgt                                                                                                                                <  2:409765/149‑1 (MQ=255)        cGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtt                                                                                                                               <  1:421205/149‑1 (MQ=255)         gAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgttt                                                                                                                              >  1:130014/1‑149 (MQ=255)          aGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttg                                                                                                                             <  2:240176/149‑1 (MQ=255)            cATTGTAACGAATGGCATCCGCCTAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATGGGGGCAAATCCACAGGTGAACTACGCTCCTCtgtttgtt                                                                                                                           <  2:143695/149‑1 (MQ=255)                      aaTGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATaaa                                                                                                                 >  1:774264/1‑149 (MQ=255)                          gCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAACCt                                                                                                             >  2:379554/1‑149 (MQ=255)                                gCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTAAGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGtt                                                                                                       >  2:710905/1‑149 (MQ=255)                                    aGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTa                                                                                                                          <  2:330393/126‑1 (MQ=255)                                    aGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTa                                                                                                                          >  1:330393/1‑126 (MQ=255)                                      tGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGAc                                                                                                 >  1:730833/1‑149 (MQ=255)                                           tGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGc                                                                                            >  1:540412/1‑149 (MQ=255)                                               ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaaaa                                                                                        <  2:540412/149‑1 (MQ=255)                                               ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCaaaa                                                                                        <  2:88005/149‑1 (MQ=255)                                               ttATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTCGTTACGCAATACACACTGGTGTTTTCGACTATGCaaaa                                                                                        >  2:540745/1‑149 (MQ=255)                                                       cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTcc                                                                                <  1:792302/149‑1 (MQ=255)                                                       cgcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTcc                                                                                <  1:163433/149‑1 (MQ=255)                                                        gcCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATACCAGCTGTATGGAAATATCGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTTTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTccc                                                                               >  1:384843/1‑149 (MQ=25)                                                         ccACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCcct                                                                              <  1:217993/149‑1 (MQ=255)                                                          cACGGGAATATGTGCGGGAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGGTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCcctc                                                                             <  1:394526/149‑1 (MQ=255)                                                                 atatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGGAGTAAAAACTGGTGTTTTCGGCTATGCAAAACAGTTTCCGTCCTCaggg                                                                      >  1:151206/1‑146 (MQ=25)                                                                 atatCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGAAGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAGCTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGc                                                                      >  1:77392/1‑149 (MQ=255)                                                                            aGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGaaaa                                                           <  1:567329/149‑1 (MQ=255)                                                                                 gtctGTAATGGGTTAAGTGATAACAGATGTCTGGAAAGATAGGGGCAAATCCACAGGGGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTg                                                      <  1:515452/146‑1 (MQ=255)                                                                                       aaTGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCACTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAgg                                                >  1:734850/1‑149 (MQ=255)                                                                                        aTGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGc                                               >  1:718171/1‑149 (MQ=255)                                                                                           ggTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCg                                            <  2:486478/149‑1 (MQ=255)                                                                                           ggTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGAGAGGCCCg                                            >  1:749395/1‑149 (MQ=255)                                                                                            gTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAACATTTGGTGAGACCCGa                                           >  2:35409/1‑149 (MQ=255)                                                                                            gTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGCGGCCCGa                                           >  2:56676/1‑149 (MQ=255)                                                                                             ttAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGAc                                          >  1:117022/1‑149 (MQ=255)                                                                                             ttAAGGGATAACAGATGTAGGGAAATATAGGGGCAAATCCATAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGAc                                          <  2:99731/149‑1 (MQ=255)                                                                                                       aCAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAAc                                <  2:117022/149‑1 (MQ=255)                                                                                                        cAGATGTCTGGAAATCTTGGGGCAAATCCACTGGTGAAGTACGCTCCTCTGTTTATTACGCAATGAACACTGGTGCTTTCGAATATGCAAAACAGTTTCCCTCCTCTCGTAATCTGGAAAAATTTGGTGAGGCCCGACAAGATCTAAcc                               <  2:582901/149‑1 (MQ=255)                                                                                                        cAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGCGGCCCGACAAGCTTTATcc                               >  2:28944/1‑149 (MQ=255)                                                                                                         aGATGCCCGGAAATATAGGGGCAAATCCACAGGTGCACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCa                              <  1:809336/149‑1 (MQ=255)                                                                                                                tGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGCTTTAACCATAAAAGa                       >  2:100110/1‑149 (MQ=255)                                                                                                                                    cacaCGTGAACTACGATCCTCTGTTTGTTACGCAATAAATACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGTCAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTgg   <  2:799186/149‑1 (MQ=255)                                                                                                                                     acaGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGc  >  2:321897/1‑149 (MQ=255)                                                                                                                                     |                                                                                                                                                     AGGCGTTCGAGCATTATAACGAATGGCATCCGCATAGTGCGCTGGGTTATCGCTCGCCACGGGAATATCTGCGGCAGCGGGCTTGTAATGGGTTAAGTGATAACAGATGTCTGGAAATATAGGGGCAAATCCACAGGTGAACTACGCTCCTCTGTTTGTTACGCAATAAAAACTGGTGTTTTCGACTATGCAAAACAGTTTCCCTCCTCACGCAATCTGGAAAAATTTGGTGAGGCCCGACAAGATTTAACCATAAAAGAACTGGCTGAAAAATTTCTGGC  >  NC_000913_3_hsa_tpiA/1651416‑1651696

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.