Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	883,665	IS1 (–) +9 bp		[mdfA]	[mdfA]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 258675	NA (NA)	63 (0.900)	47/216	0.3	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	883665 =	0 (0.000)					intergenic (‑277/‑8)	ybjG/mdfA	undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
*	?	NC_000913	= 883673	0 (0.000)	58 (0.820)	39/216	0.5	100%	coding (1/1233 nt)	mdfA	multidrug efflux system protein
	?	NC_000913	= 1050545	NA (NA)					noncoding (768/768 nt)	IS1	repeat region

GATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258539‑258675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGG  >  NC_000913/883665‑883802                                                                                                                                                                                                                                                                                     GATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGA                                                                                                                                          >  1:1057244/1‑139  ATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCCCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAA                                                                                                                                         >  1:691853/1‑139          CGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATG                                                                                                                                 <  1:89296/139‑1               CTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAA                                                                                                                            >  2:1250119/1‑139               CTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTC‑AAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAAT                                                                                                                           >  1:1474897/1‑139                                  CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTC                                                                                                                >  2:179064/1‑132                                  CCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTC                                                                                                                <  1:179064/132‑1                                                 AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTC                                                                                                                >  2:1254426/1‑117                                                 AACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTC                                                                                                                <  1:1254426/117‑1                                                           ACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTT                                                                                >  1:114359/1‑139                                                             AGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTC                                                                              >  1:1172946/1‑139                                                              GCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAATACCATCATACATTAAATCAGTAACTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCC                                                                             <  2:1057244/139‑1                                                               CTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCC                                                                            <  1:532222/139‑1                                                               CTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCC                                                                            <  2:353957/139‑1                                                                 GATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCA                                                                                                                               <  2:265180/86‑1                                                                 GATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCA                                                                                                                               >  1:265180/1‑86                                                                  ATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCT                                                                         <  1:1648236/139‑1                                                                    AGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGC                                                                                                          >  1:181668/1‑104                                                                    AGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGC                                                                                                          <  2:181668/104‑1                                                                              GCCACTGGAGCACCTCAAAAACACCATCATACATAAAATCAGTAAGTTGGCAGCATCACCGAAATTGCACACAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACCTTGCCCTCTCTGTCTGGTGCg                                                             >  2:232901/1‑138                                                                                 ACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTC                                                                                                                >  2:384749/1‑85                                                                                 ACTGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTC                                                                                                                <  1:384749/85‑1                                                                                   TGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTT                                                                                     >  2:142065/1‑110                                                                                   TGGAGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTT                                                                                     <  1:142065/110‑1                                                                                      AGCACCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAAT                                                     >  2:117710/1‑139                                                                                          CCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTAC                                                                                   <  2:255602/105‑1                                                                                          CCTCAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTAC                                                                                   >  1:255602/1‑105                                                                                          CCTCAAAAACACCATCATACATTAAATCAGTAAGGTGGCAGCATCACCGAAATTGCATGCAAAATAAATTGCCCTCCGGGGCCAGGCTTTGAGGTCAGGCAATACTTTTACCTCTCTGTCTGGGGCTTTACGAATGTTC                                                 >  2:698540/1‑139                                                                                             CAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCT                                                                         <  1:723357/112‑1                                                                                             CAAAAACACCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCT                                                                         >  2:723357/1‑112                                                                                                     CCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGTATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGC                                                                                        <  2:1170357/89‑1                                                                                                     CCATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGC                                                                                        >  1:1170357/1‑89                                                                                                       ATCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGC                                    <  1:117710/139‑1                                                                                                        TCATACATTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCA                                   >  2:1579893/1‑139                                                                                                              atTAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATA                             <  2:114359/137‑1                                                                                                                TAAATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATG                           >  2:950886/1‑139                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGAT                         >  2:27115/1‑139                                                                                                                  AATCAGTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGAT                         >  2:518646/1‑139                                                                                                                       GTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCT                                                                         <  1:552638/86‑1                                                                                                                       GTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCT                                                                         >  2:552638/1‑86                                                                                                                       GTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTC                                                                              <  1:68641/81‑1                                                                                                                       GTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTC                                                                              >  2:68641/1‑81                                                                                                                       GTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTT                                                                                     <  1:604569/74‑1                                                                                                                       GTAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTT                                                                                     >  2:604569/1‑74                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACC                   >  2:475668/1‑139                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATT                        <  1:293026/134‑1                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATT                        >  2:293026/1‑134                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTT                                                  <  2:1230104/108‑1                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTT                                                  >  1:1230104/1‑108                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACG                                                        <  1:774474/102‑1                                                                                                                        TAAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACG                                                        >  2:774474/1‑102                                                                                                                         AAGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCC                  <  1:1134779/139‑1                                                                                                                          AGTTGGCAGCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCG                 <  1:1250119/139‑1                                                                                                                                  GCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGAT                              >  2:356746/1‑118                                                                                                                                  GCATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGAT                              <  1:356746/118‑1                                                                                                                                    ATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGC       <  1:27115/139‑1                                                                                                                                    ATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGAT                              >  2:557896/1‑116                                                                                                                                    ATCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGAT                              <  1:557896/116‑1                                                                                                                                     TCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCC                                                                            >  1:1228363/1‑69                                                                                                                                     TCACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCC                                                                            <  2:1228363/69‑1                                                                                                                                      CACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTC                                                                          <  2:296171/70‑1                                                                                                                                      CACCGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTC                                                                          >  1:296171/1‑70                                                                                                                                         CGAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGG  <  1:475668/139‑1                                                                                                                                                                                                                                                                                     GATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258539‑258675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GAAATTGCATGCAAAATAAATTAGCTTCCGGTGCCAGGCTTGGACGTCAGGCGTTACTTTTCCCTCTCTGTCTGGTGCTTTACGAATTTTCAACCTATATCGGCAACGATATGATTCAACCCGGTATGTTGGCCGTGG  >  NC_000913/883665‑883802

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ 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.