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)	42 (1.060)	34/238	0.2	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)	46 (1.160)	31/238	0.2	100%	coding (1/1233 nt)	mdfA	multidrug efflux system protein
	?	NC_000913	= 1050545	NA (NA)					noncoding (768/768 nt)	IS1	repeat region

AAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/883538‑883673 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATT  <  NC_000913/1050545‑1050417                                                                                                                                                                                                                                                                           AAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGT                                                                                                                                <  1:237849/139‑1  AACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTA                                                                                                                               <  2:96695/139‑1   ACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAA                                                                                                                              <  2:99399/139‑1   ACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAA                                                                                                                              >  1:135154/1‑139          GAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCC                                                                                                                       <  2:550675/139‑1                 TAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTAT                                                                                                                <  1:176463/139‑1                 TAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTAT                                                                                                                <  1:695827/139‑1                    CTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGA                                                                                                             <  2:211409/139‑1                      ATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATA                                                                                                           <  2:587899/139‑1                              AATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTA                                                                                                   >  2:450625/1‑139                              AATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTA                                                                                                   >  2:188623/1‑139                                  ATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                               <  2:135154/139‑1                                   TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTC                                                                                              >  1:260963/1‑139                                   TGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTC                                                                                              >  2:406209/1‑139                                           TGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATG                                                                                      >  2:411767/1‑139                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCC                                                                                    >  2:620385/1‑139                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCC                                                                                    >  1:118571/1‑139                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCC                                                                                    >  1:86426/1‑139                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCC                                                                                    >  1:686071/1‑139                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                               >  1:211817/1‑128                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                               <  2:211817/128‑1                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCC                                                                                                                       <  1:785516/104‑1                                             TGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCC                                                                                                                       >  2:785516/1‑104                                              GCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCC                                                                                   >  1:389228/1‑139                                               CTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCG                                                                                  >  1:117455/1‑139                                               CTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCG                                                                                  >  1:78546/1‑139                                               CTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCG                                                                                  >  2:72936/1‑139                                               CTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATA                                                                                                           >  2:429521/1‑114                                               CTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATA                                                                                                           <  1:429521/114‑1                                                   ACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGA                                                                              <  1:188623/139‑1                                                     CGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACT                                                                            <  1:526933/139‑1                                                         GTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGT                                                                        <  1:72936/139‑1                                                                                              TTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTT                                   <  2:118571/139‑1                                                                                               TTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTC                                  <  2:711152/139‑1                                                                                                  ATTAATCTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCGGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGT                               >  2:199389/1‑139                                                                                                     AAACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCC                            >  2:802074/1‑139                                                                                                       ACTCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAG                          <  2:78546/139‑1                                                                                                         TCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                               <  1:486194/68‑1                                                                                                         TCTGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTT                                                                                               >  2:486194/1‑68                                                                                                           TGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAA                                                                                                                     <  2:389318/44‑1                                                                                                           TGCGCGATTATTATTGGCGAAGAAATTGCAGGTAATGACTCCAA                                                                                                                     >  1:389318/1‑44                                                                                                                     TTATTGGCGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCT            <  1:156984/139‑1                                                                                                                            CGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAG                                                                                            <  1:531367/52‑1                                                                                                                            CGAAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAG                                                                                            >  2:531367/1‑52                                                                                                                              AAGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGAT   <  1:198474/139‑1                                                                                                                               AGAAATTGCAGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATT  >  1:204480/1‑139                                                                                                                                                                                                                                                                           AAACTTAAAGAAAGCGTAGCTATACTCGTAATAATGTAAGAATGTGCTTAACCGTGGTTTCAGCTACAAAATTCGCTTTCTCGTTAGCTGCGCTTTTATTAAACTCTGCGCGATTATTATTGGCGAAGAAATTGCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/883538‑883673 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGACTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCTCAGATT  <  NC_000913/1050545‑1050417

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ 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.