Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,673,670	IS1 (–) +9 bp	intergenic (‑169/‑235)	mdtJ ← / → tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	257908 =	NA (NA)	31 (0.670)	27/296	0.4	100%	noncoding (768/768 nt)	IS1	repeat region
	?	NC_000913	= 1673678	0 (0.000)					intergenic (‑177/‑235)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
*	?	NC_000913	1673670 =	0 (0.000)	42 (0.910)	32/296	0.2	100%	intergenic (‑169/‑243)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
	?	NC_000913	= 1979270	NA (NA)					noncoding (1/768 nt)	IS1	repeat region

TTTTGAGTTAATTCTTAAGCTATGATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1673815‑1673670 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCG  <  NC_000913/1979270‑1979130                                                                                                                                                                                                                                                                                                 TTTTGAGTTAATTCTTAAGCTATGATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGA                                                                                                                                          <  1:566410/151‑1                 AAGCTATGATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTG                                                                                                                          <  2:207469/151‑1                    CTATGATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATT                                                                                                                       >  2:279404/1‑151                         ATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTG                                                                                                                  >  1:234195/1‑151                         ATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTG                                                                                                                  <  2:616813/151‑1                               ATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGAT                                                                                                            <  1:312197/151‑1                               ATCAGGCGTGTTCAACTACCGAGGACAAATATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGAT                                                                                                            <  2:509147/151‑1                                    GCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGG                                                                                                          <  1:184061/148‑1                                    GCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGG                                                                                                          <  2:156591/148‑1                                      GTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTT                                                                                                     >  1:237999/1‑151                                            AACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGG                                                                                               <  1:666658/151‑1                                                      GACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAG                                                                                       <  1:514102/149‑1                                                       ACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGG                                                                                    <  2:366727/151‑1                                                        CAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGA                                                                                                 >  1:655893/1‑137                                                        CAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGA                                                                                                 <  2:655911/137‑1                                                          ATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTATCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTT                                                                                 >  1:655347/1‑151                                                          ATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGCTGGTGTTTTTGAGGTGCTCCAGTGGCTT                                                                                 >  1:34546/1‑151                                                          ATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTT                                                                                 >  1:634342/1‑151                                                                     CGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATC                                                                      <  2:525760/151‑1                                                                         GACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAG                                                                    >  1:321940/1‑149                                                                             AGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTC                                                               <  2:210712/150‑1                                                                               AAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCC                                                              >  2:288587/1‑149                                                                                   AACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTG                                                        <  1:194360/151‑1                                                                                    ACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTC                                                           >  1:336653/1‑147                                                                                       CTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCA                                                    >  2:127287/1‑151                                                                                           GGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCACTCCTGTTCAGCTA                                                >  1:600755/1‑151                                                                                                ATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGAC                                           <  2:278634/151‑1                                                                                                ATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGAC                                           <  2:128380/151‑1                                                                                                ATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGAC                                           <  1:178994/151‑1                                                                                                 TTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACG                                          >  2:138428/1‑151                                                                                                 TTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACG                                          >  2:369481/1‑151                                                                                                 TTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACG                                          >  2:43120/1‑151                                                                                                 TTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACG                                          >  2:453523/1‑151                                                                                                    TAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGG                                       <  1:460524/151‑1                                                                                                        ATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGT                                   >  1:292725/1‑151                                                                                                          TATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGC                                 <  2:352956/151‑1                                                                                                                      GTTCAGGACGTTATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGACGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAA                     >  2:243738/1‑151                                                                                                                                  ATTTTCTACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGAC         <  1:242961/151‑1                                                                                                                                       CTACATTTACCCGGTGATGCTGCCAACTTACTTATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAG    <  1:709055/151‑1                                                                                                                                         ACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCG  >  1:707686/1‑151                                                                                                                                         ACATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCG  >  1:460322/1‑151                                                                                                                                          CATTTACCCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCG  >  2:438505/1‑150                                                                                                                                                                                                                                                                                                 TTTTGAGTTAATTCTTAAGCTATGATACAAATCAGGCGTGTTCAACTACCGAGGACAATTATCATCCGCGATGACGAGAAGCAACACTGCGGATAATTGTAATATTATGGACAATTTGTTCAGGACGTTATTTTCTACATTTACCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1673815‑1673670 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCGGACATCAGCG  <  NC_000913/1979270‑1979130

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ 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.