New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913_3_hsa_pgi	3583428 =	NA (NA)	54 (0.820)	42/286	0.7	90.0%	intergenic (+10/‑55)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
	?	NC_000913_3_hsa_pgi	3665150 =	6 (0.090)					coding (661/825 nt)	gadX	acid resistance regulon transcriptional activator; autoactivator

ATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_hsa_pgi/3583572‑3583428 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGACTTGG  >  NC_000913_3_hsa_pgi/3665150‑3665297                                                                                                                                                                                                                                                                                                       ATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCT                                                                                                                                                  <  1:71262/149‑1   AGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGT                                                                                                                                                <  1:777093/149‑1   AGCGCTGAAGTCCGGCGGTGCTTTGGCCGTTACGCACCACCCCGTCAGGAGCTGAACAGCAGGCACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGT                                                                                                                                                <  2:1044208/149‑1       cgGATGTCCGGCGGTGCTTTCTCCATCACGCACCACCCCTGCAGTAGGCGAACATGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCGGTGATA                                                                                                                                            <  1:828853/147‑1           TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCA                                                                                                                                        <  1:315180/149‑1             TCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAGGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCAGCCGCTGTGATATCCCCA                                                                                                                                      >  2:817854/1‑149                     TGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTG                                                                                                                              <  2:356751/149‑1                         TTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAAC                                                                                                                          >  1:685420/1‑149                                  ACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGAAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAAT                                                                                                                 >  2:1035701/1‑149                                      gCCACCCCGTCAGTAGCTTAACAGGAGGGACAGCTGAGAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCGCCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAA                                                                                                             >  2:1001373/2‑149                                      ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCA                                                                                                                                        <  1:935871/122‑1                                      ACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCA                                                                                                                                        >  2:935871/1‑122                                       CCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAA                                                                                                            <  2:1016609/149‑1                                        CACCCCGTCAGTAGCTGAACAGGAGGGACGGCTGATAGGAACAGGAGCCAGTGGAGCCCCTAAAAAACACTATCATACACTAAATCGGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTCAAAA                                                                                                           >  1:958293/1‑149                                            CCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCA                                                                                                       <  1:736546/149‑1                                            CCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCA                                                                                                       >  1:481526/1‑149                                            CCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCA                                                                                                       <  1:343643/149‑1                                                         cACAGGACGGACAGTTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCTTCATACACTTAATCATTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTTTTTTAAAATCCATGTATAACAATAA                                                                                          <  2:609039/148‑1                                                           CAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACAATGTATAACAATAAGT                                                                                        >  1:648689/1‑149                                                             GGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTCGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTG                                                                                      <  2:504594/149‑1                                                                   ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCCCAGGATACTGCAACTCCCTTAATTGAAAAACCATGTATAACAATAAGTTGCAATGC                                                                                >  2:165772/1‑149                                                                   ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGC                                                                                >  1:750575/1‑149                                                                           TAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCA                                                                        >  2:719400/1‑149                                                                             GAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCAACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATT                                                                      >  2:807099/1‑149                                                                                      GCCACGTGAGCACCTCAAAAACACCATCATACACCAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCA                                                             <  2:557512/149‑1                                                                                        CACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGT                                                           <  1:424292/149‑1                                                                                         ACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAATA                                                          >  2:502477/1‑149                                                                                           TGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAG                                                        >  1:15115/1‑149                                                                                                    TCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGA                                               >  2:902686/1‑149                                                                                                     CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAA                                              <  1:767043/149‑1                                                                                                     CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAA                                              <  1:719400/149‑1                                                                                                      AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAAT                                             >  1:889667/1‑149                                                                                                      AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAAT                                             >  2:1085685/1‑149                                                                                                          ACACCATTATACACTAAAGCAGTAAGTCGGCAGCATCAGCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGA                                         <  2:297897/149‑1                                                                                                            ACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATG                                       >  1:195257/1‑149                                                                                                             tCATCGTACACTAAATCAGTAAGTGTGCAGCATCACCTGCTGGGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTTCAAAGCACGTTGCATTCTACAGTCAGTAATCAACTGAAAATAGGATGT                                      <  2:249553/148‑1                                                                                                                   TACACTAAATCAGTAAGTGGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTC                                <  2:685420/149‑1                                                                                                                      ACTAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTC                             >  2:541279/1‑149                                                                                                                        cAAATCAGTAAGTGGGCAGAATCACCGGCTGTGATATTCACAGGATACTGCAACTTGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGC                           <  2:831311/148‑1                                                                                                                        TAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGC                           <  1:1029498/149‑1                                                                                                                        TAAATCAGTAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGC                           <  2:750575/149‑1                                                                                                                                TAAGTTGGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTT                   >  2:916381/1‑149                                                                                                                                   ttcGGCAGCATCACCCGTGGTGATAGCCACAGGATACTGCAACTCGTTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTC                <  2:242040/146‑1                                                                                                                                   gttgcgcGCATCCCCCGATGTACTATCCCCAGGTTACTGCATCTCTTTTAATTGAAAAACCATGTATAACAATACGTTGCAAAGCACGTTGCATTCTCCACTCAGTTAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTC                <  1:518120/142‑1                                                                                                                                      GGCAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCACCTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTT             >  1:209608/1‑149                                                                                                                                        CAGCATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAA           <  1:681254/149‑1                                                                                                                                            ATCACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGA       >  1:679936/1‑149                                                                                                                                              CACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGACT     >  2:1038090/1‑149                                                                                                                                              CACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAA           <  1:883925/143‑1                                                                                                                                              CACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAA           >  2:883925/1‑143                                                                                                                                               ACCCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGACTT    >  1:1108159/1‑149                                                                                                                                               ACCCGCTGTGATATCCACAGGATACTGCAACTCGCTCAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTATGCAACTGTGAATATGAGGTCGCTTCATCGCGCAATTTTTTCTTTAACAGACTT    <  2:943790/149‑1                                                                                                                                                CCCGCTGTCATATCCACAGGATACTGCAACTCCCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACTCGCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGACTTG   <  1:502477/149‑1                                                                                                                                                 CCGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGACTTGG  >  1:65199/1‑149                                                                                                                                                                                                                                                                                                       ATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913_3_hsa_pgi/3583572‑3583428 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CGCTGTGATATCCACAGGATACTGCAACTCGCTTAATTGAAAAACCATGTATAACAATAAGTTGCAAAGCACGTTGCATTCTACACTCAGTAAGCAACTGTGAATATGATGTCTCTTCTTCGCGCAATTTTTTCTTTAACAGACTTGG  >  NC_000913_3_hsa_pgi/3665150‑3665297

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.