Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,743,880	IS1 (–) +9 bp	coding (424‑432/1374 nt)	mdtK →	multidrug efflux system transporter

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 258675	NA (NA)	42 (0.850)	36/298	0.7	100%	noncoding (1/768 nt)	IS1	repeat region
	?	NC_000913	1743880 =	0 (0.000)					coding (424/1374 nt)	mdtK	multidrug efflux system transporter
*	?	NC_000913	= 1743888	0 (0.000)	46 (0.940)	43/298	0.3	100%	coding (432/1374 nt)	mdtK	multidrug efflux system transporter
	?	NC_000913	1978503 =	NA (NA)					noncoding (768/768 nt)	IS1	repeat region

CAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258526‑258675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTCGGTATGCCTGAGCTCGGTGGC  >  NC_000913/1743880‑1744026                                                                                                                                                                                                                                                                                                           CAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCC                                                                                                                                                    <  2:601507/151‑1  AGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCT                                                                                                                                                   >  2:604924/1‑151     GATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTT                                                                                                                                                <  1:478012/151‑1        AGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCT                                                                                                                                              <  2:621436/150‑1                TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTG                                                                                                                                     >  2:739604/1‑151                     GGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGT                                                                                                                                >  1:695055/1‑151                                    GTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGTAGCCCCTCAAAATCACCATCATTCACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGT                                                                                                                 <  2:559296/151‑1                                        CGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGG                                                                                                             >  1:153696/1‑151                                          CACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCA                                                                                                           <  2:732791/151‑1                                                      AGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCG                                                                                               <  1:466676/151‑1                                                       GTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGG                                                                                              <  2:163131/151‑1                                                           CTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTAT                                                                                          >  1:256182/1‑151                                                                CAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGCAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGCGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTA                                                                                      >  2:18073/1‑150                                                                     GGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGC                                                                                <  2:618303/151‑1                                                                       GACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTT                                                                              <  2:64349/151‑1                                                                       GACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTT                                                                              >  1:481896/1‑151                                                                       GACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTT                                                                              <  1:57073/151‑1                                                                            CTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCG                                                                         >  1:605067/1‑151                                                                              GATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGG                                                                        <  1:159181/150‑1                                                                                      CAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGG                                                                >  2:26122/1‑150                                                                                         AAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGA                                                             <  1:515855/150‑1                                                                                            CCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACAT                                                         <  1:674022/151‑1                                                                                             CACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATC                                                        >  1:408403/1‑151                                                                                             CACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATC                                                        >  2:517694/1‑151                                                                                                TGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCG                                                     >  1:591324/1‑151                                                                                                   AGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCATCCAGGTTGCCCGTAACCAGTGTGAAGGGCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCG                                                     <  2:291591/148‑1                                                                                                     CACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAA                                                <  1:161911/151‑1                                                                                                          CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATA                                           <  2:745108/151‑1                                                                                                          CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATA                                           <  1:199843/151‑1                                                                                                          CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTAT                                            >  2:35644/1‑150                                                                                                          CAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTAT                                            >  1:712415/1‑150                                                                                                           AAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATAT                                          >  1:481169/1‑151                                                                                                            AAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATC                                         <  2:591321/151‑1                                                                                                             AAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCT                                        >  2:621665/1‑151                                                                                                                      CATGCACTAAATCAGTAAGTTGGCAGCATCGCCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATG                               <  2:59260/151‑1                                                                                                                            CTAAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCAT                          <  1:332982/150‑1                                                                                                                              AAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGTCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTC                       <  2:481893/151‑1                                                                                                                              AAATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTC                       <  1:260364/151‑1                                                                                                                               AATCAGTAAGTTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTCG                      >  1:714633/1‑151                                                                                                                                         TTGGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGGAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTCGGTATGCCT              >  2:282074/1‑149                                                                                                                                           GGCAGCATCACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTCGGTATGCCTGAGC          <  1:417847/151‑1                                                                                                                                                   CACCCTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTCGGTATGCCTGAGCTCGGTGGC  >  1:736622/1‑151                                                                                                                                                                                                                                                                                                           CAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACAGGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAAGTTGGCAGCATCACC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/258526‑258675 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTGTTCTTCCAGGTTGCCCGTAACCAGTGTGAAGGTCTGGCAAAAACCAAGCCGGGTATGGTAATGGGCTTTATCGGCCTGCTGGTGAACATCCCGGTGAACTATATCTTTATTTATGGTCATTTCGGTATGCCTGAGCTCGGTGGC  >  NC_000913/1743880‑1744026

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ 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.