New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_pgi	= 3584195	NA (NA)	20 (0.370)	18/270	NT	37.7%	intergenic (+15/‑1)	insB1/yrhA	IS1 transposase B/pseudogene, interrupted by IS1E
	?	NC_000913_3_hsa_pgi	= 3665158	33 (0.620)					coding (653/825 nt)	gadX	acid resistance regulon transcriptional activator; autoactivator

AATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAT  >  NC_000913_3_hsa_pgi/3584048‑3584343                                                                                                                                                    |                                                                                                                                                      aaTTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCg                                                                                                                                                      >  1:1001270/1‑149 (MQ=11) aaTTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCg                                                                                                                                                      >  1:652501/1‑149 (MQ=11)         ggCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTaaa                                                                                                                                              <  1:86755/149‑1 (MQ=35)              taCCTGAATCTGAGGCAGCACCGGGCACGGCTGGGACGGTAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTAATAGGGCGTTAATTTAACATAAAACTCTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTaa                                                                                                                                         <  2:616762/148‑1 (MQ=11)              aaCCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCAGCACGAACAACTACACCTGCAGTATCTGAACATCAGACACTATCAATAAGTTGGAGTCATTACCTACATTAAAAGTaa                                                                                                                                         <  2:715661/149‑1 (MQ=11)               aCCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAAc                                                                                                                                        >  1:43461/1‑149 (MQ=38)               aCCTGAAGCTGAGGCAGCAACTGTCAAGGCTGGGACGGAAGTCGCTGTCGTTTTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAAc                                                                                                                                        <  2:279546/149‑1 (MQ=11)                 cTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGCCATTACCGACATTAAAAGTAACtt                                                                                                                                      >  1:637757/1‑149 (MQ=255)                 cTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGAAAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACtt                                                                                                                                      >  1:345806/1‑149 (MQ=255)                  tGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTCTCAATAAGTTGCAGTCATTACCGACATTAAAAGTAACttt                                                                                                                                     >  2:301769/1‑149 (MQ=255)                      tCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGGAACTTTTTTg                                                                                                                                 >  1:846324/1‑149 (MQ=255)                            gcagcaCCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTa                                                                                                                           <  2:1004329/149‑1 (MQ=255)                                caCCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTagagg                                                                                                                       >  1:170720/1‑148 (MQ=255)                                caCCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAgaga                                                                                                                       >  1:477239/1‑149 (MQ=255)                                   cTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATAGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTTGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGataa                                                                                                                    >  2:440890/1‑149 (MQ=255)                                     ggCACGGCTGGGACGGAAGTCGCTGTCTTTCCCAAAATAGGTGGCGCTGCATCACAAAGTCCTCGGGCATTATCTGAACATAACACACTATCACTAAGTTAGAGTCCTTCACAACATTAAACGTAACCTTTTTAAAAATAGAGccaata                                                                                                                  >  2:231016/1‑149 (MQ=14)                                         cGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATTACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGTGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTgg                                                                                                              <  2:189777/149‑1 (MQ=255)                                                  gggAAGTCGCTGTCGTTGTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGaaaa                                                                                                     <  2:595677/148‑1 (MQ=255)                                                                 ttCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGtt                                                                                     >  2:734259/1‑149 (MQ=255)                                                                   ctcAAATTCGTTGGAGCTGTATGACAGAGTCATCGGGCATTATCTGAACATAATACACTATCAATAAGTTGGCGTCTTTACAGTCATTAAAAGTAACTGTTTTGAAATTAGAGATAATATTTGCACAGAAAATA‑TATTCAGTTCGTTTa                                                                                   <  2:17358/149‑1 (MQ=21)                                                                      gaaaTCGGTGGAGCTGCATGACACAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGACATTACCGACATTGAAAATAACTTTTTTGAAATTAGAGACAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTg                                                                                >  2:927540/2‑149 (MQ=25)                                                                      aaaaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTg                                                                                >  1:705946/1‑149 (MQ=255)                                                                       aaaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGa                                                                               <  2:343114/149‑1 (MQ=255)                                                                        aaTCGGTGTAGCTGCATGACAAAGTCATCGGGCACTATCTGAACATAAAACACTACCAATAAGATGGAGTTATTATCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGAt                                                                              <  1:892304/149‑1 (MQ=25)                                                                        aaTCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTTAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTATTGAt                                                                              >  2:76479/1‑149 (MQ=255)                                                                                          aCAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTATCTTCAGTCTTaaaa                                                            >  1:298949/1‑148 (MQ=255)                                                                                                 cATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAATTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCa                                                     >  1:429282/1‑149 (MQ=255)                                                                                                 aagcGGGTATTATATAAACAGAAAAGAATATCAATAGGTTGGAATCATAACCGAAATTCAAAGTAACTTTTTTGAAATTAGAGTTAATAAAAAAACAAAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTCAAACGAAATCa                                                     <  2:874250/146‑1 (MQ=255)                                                                                                     gggCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACAAAATCATGGa                                                 >  1:453097/1‑149 (MQ=255)                                                                                                           tATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGt                                                                                 >  2:263585/1‑111 (MQ=255)                                                                                                           tATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGt                                                                                 <  1:263585/111‑1 (MQ=255)                                                                                                             tCTTAACATAAGACAATAGCAATGAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAgttgtt                                         <  2:640331/149‑1 (MQ=255)                                                                                                                gAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCat                                      >  1:459486/1‑149 (MQ=255)                                                                                                                 aaCATAAAACACTATCAATAAGTTGGAGACAATACCGACAATAAAAGAAACTCTTTTGAAACGCGGTATAAAAATGGGAC‑GAAAAGATTATTCAGTTGGTTTAGTGATTGCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCata                                     <  2:590186/149‑1 (MQ=19)                                                                                                                  aCATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCataa                                    >  1:878888/1‑149 (MQ=255)                                                                                                                        aaCACTATCAATAAGTTGGAGTCATTAGCGACATTAAAAGTAACTTTTTTGAAATTAGGGATAATATTGGCGCAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAAAGAAATCATGTGCAGTGGTTCATAATAATCa                              >  2:344846/1‑149 (MQ=255)                                                                                                                             tATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAgg                         >  1:501083/1‑149 (MQ=255)                                                                                                                               tCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACACTTGTTCATAATAATCAAAAAGaa                       >  1:176750/1‑149 (MQ=255)                                                                                                                                       ttGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGCGATAAAAATGGCACAGAAAATA‑TATGCTGTTCGTTTAATGATTTCTCTTCGTTCTAAAACGAAATAATTGACAGTTCTTCATAATACTCCAAACGCAACaaaagt               >  2:314319/1‑147 (MQ=255)                                                                                                                                        tGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATc              >  2:140175/1‑149 (MQ=255)                                                                                                                                           gttCATAACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCAtt           <  2:43461/147‑1 (MQ=255)                                                                                                                                           ggTCTTTACCGTCATTAAAAGTAACTTTTTTGAAATTAGTGATATTATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCAtt           <  1:301769/148‑1 (MQ=255)                                                                                                                                           ggTCATTGCCGACATTAAAGGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCAtt           <  1:474183/148‑1 (MQ=255)                                                                                                                                                    cGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCTTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTTATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAt  >  1:211627/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                      AATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAAGTCGCTGTCGTTCTCAAAATCGGTGGAGCTGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCGACATTAAAAGTAACTTTTTTGAAATTAGAGATAATATTGGCACAGAAAATA‑TATTCAGTTCGTTTAGTGATTTCTCTTCATTCTTAAACGAAATCATGGACAGTTGTTCATAATAATCAAAAGGAAACAAAAATCATTGTAAACCAT  >  NC_000913_3_hsa_pgi/3584048‑3584343

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.