Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,673,883	IS5 (–) +4 bp	intergenic (‑382/‑27)	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	1673883 =	0 (0.000)	46 (0.780)	42/298	0.8	100%	intergenic (‑382/‑30)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
	?	NC_000913	= 2290113	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region
*	?	NC_000913	= 1673886	0 (0.000)	51 (0.860)	45/298	0.6	100%	intergenic (‑385/‑27)	mdtJ/tqsA	multidrug efflux system transporter/pheromone AI‑2 transporter
	?	NC_000913	2101749 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region

GCGAGAATAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1674031‑1673883 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT  <  NC_000913/2290113‑2289970                                                                                                                                                                                                                                                                                                       GCGAGAATAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAG                                                                                                                                                 <  2:433757/150‑1  CGAGAATAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGA                                                                                                                                               <  1:432221/151‑1     GAATAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGG                                                                                                                                            >  1:452560/1‑151      AATAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGT                                                                                                                                           >  1:574819/1‑151        TAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGC                                                                                                                                         >  1:226536/1‑151           ACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAA                                                                                                                                      <  1:14295/151‑1                 ctATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTC                                                                                                                                >  1:869264/3‑151                          CGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATG                                                                                                                       <  2:480183/151‑1                          CGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATG                                                                                                                       >  2:216370/1‑151                          CGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATAT                                                                                                                        <  2:659333/150‑1                             CGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                                                                                    <  2:12541/151‑1                               GCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATG                                                                                                                       >  2:808532/1‑146                                          ACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCAT                                                                                                       >  1:187898/1‑151                                           CCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATC                                                                                                      >  2:274473/1‑151                                             GCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTG                                                                                                    <  1:185513/151‑1                                               AGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGG                                                                                                   >  2:78557/1‑150                                                GAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGG                                                                                                   >  1:767364/1‑149                                                    ATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCAT                                                                                             >  2:126699/1‑151                                                          ACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACA                                                                                       <  1:50053/151‑1                                                           CCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAAC                                                                                        >  2:711779/1‑149                                                            CAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGG                                                                                     >  2:883252/1‑151                                                                 TTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTC                                                                                 >  2:327874/1‑150                                                                   CCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATC                                                                              <  1:174466/151‑1                                                                   CCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATC                                                                              >  2:73976/1‑151                                                                    CCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCA                                                                             <  1:628803/151‑1                                                                       ACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                          <  1:78674/151‑1                                                                                   TTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTT                                                               >  2:771666/1‑150                                                                                       TAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCT                                                           <  2:645616/150‑1                                                                                        AGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTT                                                          <  1:808635/150‑1                                                                                               TGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGAC                                                   <  1:476703/150‑1                                                                                                GAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTGTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAG                                                 <  1:238878/151‑1                                                                                                            CGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCA                                      <  1:420625/150‑1                                                                                                            CGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCA                                      <  1:350912/150‑1                                                                                                             GGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGT                                    <  2:326197/151‑1                                                                                                             GGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGACATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGT                                    <  1:518003/151‑1                                                                                                                      ATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCG                            <  1:285482/150‑1                                                                                                                         CTTGTCCCCGTTTTTTCTTCCTTTGCTAACGAAGGAGCTAACAAGTCCCTGATATGACATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCCCCGACAGTGAATTCAGGAGTAAGCGCCG                            >  2:475799/1‑147                                                                                                                             TCCCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACC                     <  2:852904/150‑1                                                                                                                               CCCGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGA                  <  2:434207/151‑1                                                                                                                                 CGTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAA                <  2:825884/151‑1                                                                                                                                  GTTTTTTCTTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAA               <  1:654917/151‑1                                                                                                                                          TTCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTT       >  2:763089/1‑151                                                                                                                                           TCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGATCAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTT        <  1:327916/149‑1                                                                                                                                           TCCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTT        <  1:845267/149‑1                                                                                                                                            CCTTTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCT     <  1:76178/151‑1                                                                                                                                               TTGCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT  >  2:249865/1‑151                                                                                                                                                                                                                                                                                                       GCGAGAATAAACGGCACGATGATCTCGGCGGCAAAACGGATACCGCAGAGAATAATGACCAGCATTCCCAACATAATGACGATTTTTAGGCCATTGAGCGTGATGATCGGCTTTGCCATGCTTGTCCCCGTTTTTTCTTCCTTTGCTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  NC_000913/1674031‑1673883 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT  <  NC_000913/2290113‑2289970

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