New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_pgi	= 3584195	NA (NA)	76 (1.160)	56/286	0.2	97.4%	intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E
	?	NC_000913_3_hsa_pgi	= 3665158	2 (0.030)					coding (653/825 nt)	gadX	acid resistance regulon transcriptional activator; autoactivator

ATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAT  >  NC_000913_3_hsa_pgi/3584049‑3584343                                                                                                                                                    |                                                                                                                                                     aTTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGa                                                                                                                                                    <  2:557938/149‑1 (MQ=31)    gAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGACTCATTACCGACAt                                                                                                                                                 >  1:543564/1‑149 (MQ=17)         gCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTaaaa                                                                                                                                            <  2:68065/149‑1 (MQ=35)         gCATAACATGAATCTGAGGCAGCACCTGGCACGGATGGGAAGGCAGTAGCTATAGATGTCCAAATCCTAGGACCTGAATGACAAAGGCATCGGTCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTaaaa                                                                                                                                            <  2:1087568/149‑1 (MQ=11)          cATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAg                                                                                                                                           <  2:35419/149‑1 (MQ=35)           aTAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGt                                                                                                                                          >  1:884952/1‑149 (MQ=35)                   aaTCTGAGGGATGACCTGGCACGGCTGGGACGGAAGTCGCGGTCGTTCTCAAAAGCGGTGGAGATGCATGACAAAGTCATCGTGCATTATCTGATCATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACttttt                                                                                                                                  <  2:1126050/149‑1 (MQ=14)                       tGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGaa                                                                                                                              >  1:1028725/1‑149 (MQ=255)                            cagcaCGTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTag                                                                                                                         <  2:314349/149‑1 (MQ=255)                              gcaACTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATTACAAAGTCATCGGGCATTATCTGAACATGAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATGagag                                                                                                                       <  2:986605/149‑1 (MQ=255)                                     gCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAatat                                                                                                                <  1:404330/149‑1 (MQ=255)                                      cACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCAGTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTNAAAGTAGCTTTTTTGAAANTAGAGATAATAtt                                                                                                               <  2:979903/149‑1 (MQ=255)                                       aCGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTTAACATAAAACACTAT‑CAATAAGTTGGAGGCATTACCGACATTAAAAGTAACTTTTTTGAAATTAAAGAGAATATTg                                                                                                              >  1:362774/1‑149 (MQ=255)                                                 cGGAAGTCGCTTTCGTTCTCAAAATCGGTGTACCTGCATTACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATACGTTGGAGTCACGACCGACATTAACAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGaaaa                                                                                                    <  1:507163/149‑1 (MQ=18)                                                    aaGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGAATTACCCGCACCCAAAAGAATATGCGATACGGT‑GAGTCATTACCGACATTAAATGTATCTTTTTTGAAATTCGAGATAATATTGGCACAGAAAatat                                                                                                 >  1:1114902/1‑149 (MQ=18)                                                     aGTTGCTGTCGTTCTCAGATTCGGTGGGGCTGCATGACAAAGTCATCGGGCATTATCTGAACTTAACACACTAT‑TGAGAAGTTGGAGTCATTACCGACAGTAAAAGTAACTTTTGTGAATTTAGAGATAGTTTTGGCACAGAAAatata                                                                                                <  2:454895/149‑1 (MQ=18)                                                         gCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCa                                                                                            <  2:1028725/149‑1 (MQ=255)                                                           tGTCGTTCTCAAAATCGGTTCAGGGTGGGAACAAAGTGATGGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGt                                                                                          <  2:519789/149‑1 (MQ=21)                                                             tCGTCCGCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAATGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTc                                                                                        <  2:289337/149‑1 (MQ=255)                                                                   tcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTgg                                                                                                             <  2:420909/122‑1 (MQ=255)                                                                   tcAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTgg                                                                                                             >  1:420909/1‑122 (MQ=255)                                                                    cAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGt                                                                                 <  1:616586/149‑1 (MQ=255)                                                                           ggTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATAtt                                                                                              >  1:663059/1‑129 (MQ=255)                                                                           ggTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATAtt                                                                                              <  2:663059/129‑1 (MQ=255)                                                                               gAGCTGCATGACAAAGTCATCGGGCTTTATCTGAACATAAAACACTAG‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTc                                                                      <  1:23293/149‑1 (MQ=255)                                                                                 gCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCAt                                                                    <  1:723749/149‑1 (MQ=255)                                                                                 gCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCAt                                                                    >  1:1130239/1‑149 (MQ=255)                                                                                   tGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTc                                                                  <  1:483888/149‑1 (MQ=255)                                                                                     cATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGCACTTGCTCAAAATATTGGCACAGAAAATATATTCAGTTCGTTTCGTGATTTCTCTTCcttctt                                                                >  1:262311/1‑149 (MQ=21)                                                                                        gACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTaaa                                                             <  2:543564/149‑1 (MQ=255)                                                                                         aCAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAAc                                                            >  1:11963/1‑149 (MQ=255)                                                                                         aCAAAGTCATCGGGAATTAGCTGAACAGAAAACACTAA‑CAATAAGTGGGAGTCATTACCGACACTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAAc                                                            <  2:9534/149‑1 (MQ=255)                                                                                           aaaGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGa                                                          >  1:711302/1‑149 (MQ=255)                                                                                           aaaGTCATCGGGCATCTTCTTAACAGAAAACACTAT‑CAAAAAGTGGGAGTCGTTACCGACATTAAAAGTAACTTTTTTTATTTTAGATATAGCATATGCATACATAGTATATTCAGTTCATGTAGTGATTTCTATTCATTCTTACACGa                                                          >  2:673383/1‑149 (MQ=255)                                                                                           aaaGTCATCGGGCAGTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGa                                                          <  2:1114902/149‑1 (MQ=255)                                                                                             aGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGaaa                                                        <  2:711302/149‑1 (MQ=255)                                                                                                 aTCGGGCATTATCTGAACATAAAACACTAT‑CACTAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCAt                                                    <  1:19636/149‑1 (MQ=255)                                                                                                     ggCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGAc                                                >  1:763287/1‑149 (MQ=255)                                                                                                      gCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTTTTAAACGAAATCATGGACa                                               >  2:92483/1‑149 (MQ=255)                                                                                                         ttATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTGATTCTTAACCGAGATCGTGTACAttt                                            >  1:1099844/1‑149 (MQ=38)                                                                                                             cTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTc                                        <  1:305920/149‑1 (MQ=255)                                                                                                              tGAACATAAAACACTAT‑CAATGAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCa                                       <  1:217554/149‑1 (MQ=255)                                                                                                              tGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCa                                       >  2:742654/1‑149 (MQ=255)                                                                                                                      aaaCACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATc                               <  1:973914/149‑1 (MQ=255)                                                                                                                       aaCACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCa                              >  1:803517/1‑149 (MQ=255)                                                                                                                              t‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAACTCATCGACAGTTGTTCATAATAATCATAGGGaa                       >  2:507634/1‑149 (MQ=255)                                                                                                                                 aaTAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAAc                     >  1:448338/1‑149 (MQ=255)                                                                                                                                   tAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACaa                   >  1:1031933/1‑149 (MQ=255)                                                                                                                                       ttGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCTTAATATTCAAAAGGCaaaaaattc               >  2:850935/1‑146 (MQ=255)                                                                                                                                             tCATTACGGACATTAAAAGTAACTTTTTTGAAATTAGAGATAAAAATGGAACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGt         <  2:11963/149‑1 (MQ=255)                                                                                                                                                    cGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAt  >  1:757560/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                     ATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTAT‑CAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATATATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAT  >  NC_000913_3_hsa_pgi/3584049‑3584343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ 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.