Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,979,486	IS5 (+) +4 bp	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1979486 =	0 (0.000)	82 (1.710)	45/282	0.1	100%	intergenic (‑271/‑267)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	2101749 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region
*	?	NC_000913	= 1979489	0 (0.000)	49 (1.020)	41/282	0.1	100%	intergenic (‑274/‑264)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	= 2290113	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region

AGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1979357‑1979489 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGA  <  NC_000913/2290113‑2289981                                                                                                                                                                                                                                                                            AGGAATACTCCAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGAGAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCG                                                                                                                             <  2:297109/143‑1  GGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGA                                                                                                                            <  1:46949/143‑1   GAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACACCAAACTAAGGAAGGTGCGAA                                                                                                                           >  1:171760/1‑143      TAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAA                                                                                                                        <  1:580447/143‑1        ATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACGGCACAACAAACTAAGGCAGGTGCGAACAAGT                                                                                                                      >  1:738833/1‑143          CGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCC                                                                                                                    <  1:427613/143‑1          CGAAAAGGCATCTTCCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCC                                                                                                                    <  1:135701/143‑1           GAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCC                                                                                                                   <  2:472499/143‑1            AAATGGGATGTTGCGCGCAGTCAAAACAACCCACCGTAAATTAGTGTGTTCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCT                                                                                                                  <  1:324791/143‑1            AAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCT                                                                                                                  <  1:792181/143‑1              ATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGGCCCTGA                                                                                                                <  2:402621/143‑1                   ATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGA                                                                                                           <  1:528064/143‑1                     GTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGA                                                                                                         >  1:615862/1‑143                        GCGCACAGTCAAAATAACCTGACGTAAATAATCATCTGCTATAAATAATCACTTTCCTGCAATACCAGACAAGGTGTTTTTAAACAGACACTTACCGCACAACAAACGAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCA                                                                                                      <  2:200485/143‑1                          GCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAACCTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATG                                                                                                    >  1:754943/1‑143                              AGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATCTGAGATCATGTTTG                                                                                                >  1:761156/1‑143                               GTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACGAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGT                                                                                               >  1:292218/1‑143                               GTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCGATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGCTATGAGACCATGCTTGT                                                                                               >  1:292232/1‑143                               GTCAAAATAACTCACAGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGT                                                                                               <  1:529663/143‑1                                  AAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAA                                                                                                                        <  2:45189/115‑1                                  AAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAA                                                                                                                        >  1:45189/1‑115                                           CACCGTAAATAATCATCTGCTATAAATAATCACTTGCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCA                                                                                   <  2:572802/143‑1                                                  AATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACA                                                                            <  1:661390/143‑1                                                     AATCATCTTCTATCAATAATCATTTTCAACCAATACCAGATAAGCTATTTTTAAACAGACACCTACCGCACAACAAACTAAGGAAGGTGCGAAGAAGGCCCGGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGG                                                                         <  2:62308/143‑1                                                        CATCTGCTATCCATAATCACTTTCATGCAATACCAGATAAGCTATCTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTC                                                                      <  1:1512/143‑1                                                         ATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTCGAGCCATAGAACCGGGTTCA                                                                     >  2:844486/1‑143                                                              CTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTACGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATG                                                                >  2:387494/1‑143                                                              CTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATG                                                                >  1:498923/1‑143                                                              CTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACACACACTTACCGCACAACAAACTACGGCAGGTGCGAACAAGTCCCGGATATGAGATCATGTTTGCAATCTGGAGCCATAGAGCAGGGTTCATagcg                                                                >  2:387977/1‑139                                                                 TAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGT                                                             >  1:721110/1‑143                                                                  AAATAATCACTTTCGTGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACATAAAACTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTC                                                            <  2:57201/143‑1                                                                        TCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGACCAGGGTTCATCATGAGTCATCAAC                                                      >  2:359125/1‑143                                                                         CACTGTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACT                                                     <  2:590284/143‑1                                                                            TTTCATGCAATACCAGATAAGCTATTTTTAAACAGCCACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTTATATGACATCACGTTTGTCATCTGGAGCCATAGAACAAGGTTGATCATGCGTCATCCACTCAC                                                  >  2:594331/1‑143                                                                             TTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACC                                                 >  1:688518/1‑143                                                                                            ATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAA                                  <  1:736235/143‑1                                                                                                 CTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAG                             <  1:13329/143‑1                                                                                                 CTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAG                             <  1:485912/143‑1                                                                                                 CTATTTTTAAACAGACACTTACCGCACAACAAACTAAGCAAGATGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGGTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAG                             >  2:681402/1‑143                                                                                                  TATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGCTCCTGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAATCATCAACTTACCTTCGCCCCCATTGTAGTCAGC                            >  1:543663/1‑143                                                                                                   ATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCGGACAGTGAATTCAGCA                           >  2:163152/1‑143                                                                                                      TTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTGACCTTCGCCGACAGTGAATTCAGCAGTA                        <  1:372867/143‑1                                                                                                           ACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAAATCATGTTTGACATCTGGAGCCATAGAACAGGGTTCATCATGAGTCCACAACTTACCTACGCCGACAGTGACTTCAGCAGTACGCGa                   >  2:60312/1‑142                                                                                                                   ttcctGCACTACAAACTAGGGTAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATTATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAGGCGCCGTCAGAC           <  2:515552/138‑1                                                                                                                   TTACCGCGCAACAAGCGATGGAAGGTGCGAACAGGTCGCTGATATGGGATCATGTTGGTCATCTCGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGAC           <  2:708653/143‑1                                                                                                                       CGCACAACAAACTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGA       <  1:421767/143‑1                                                                                                                          ACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTACGCGCCGTCAGACCAGAAAA    >  1:27016/1‑143                                                                                                                          ACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAA    <  2:697864/143‑1                                                                                                                            AACAAACTAGGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGGTCATCATGAGTCATCAACTTACCTCCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGA  <  2:824547/143‑1                                                                                                                                                                                                                                                                            AGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1979357‑1979489 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGA  <  NC_000913/2290113‑2289981

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ 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.