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)	33 (1.040)	26/270	0.3	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)	44 (1.390)	34/270	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

AAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1979353‑1979489 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  <  NC_000913/2290113‑2289966                                                                                                                                                                                                                                                                                               AAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAA                                                                                                                                          >  4:35432/1‑149         ATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCC                                                                                                                                  <  3:13159/149‑1           AATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCT                                                                                                                                 >  4:19546/1‑148            ATCGAAATGGGATGTTGCGCACAGTCAAAATAATTCACCTTAAATAATCATCTTCTTTAAATAATCACTTTCATGTATTACCATATAATCTATTTTTAAACTGAAACTTACCGAACAACAAACTAATGAATGTGCGAAAAAGTCCCTGA                                                                                                                               <  6:53945/149‑1               GAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATAT                                                                                                                            >  2:96786/1‑149                 AATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGA                                                                                                                          <  4:30926/149‑1                            GCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTT                                                                                                                <  3:17258/148‑1                              GCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGT                                                                                                              >  4:47161/1‑148                                 CAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATC                                                                                                          <  3:19546/149‑1                                   GTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGA                                                                                                                               <  1:139000/126‑1                                   GTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGA                                                                                                                               >  2:139000/1‑126                                      AAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGA                                                                                                      <  8:45087/148‑1                                       AAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGC                                                                                                    >  5:110509/1‑149                                        AATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAA                                                                                                                                                  >  7:118503/1‑102                                        AATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAA                                                                                                                                                  <  8:118503/102‑1                                                             ATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAACGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                              <  1:96786/149‑1                                                                  CTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCAT                                                                         <  1:111334/149‑1                                                                   TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATA                                                                                                <  2:138095/125‑1                                                                   TATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATA                                                                                                >  1:138095/1‑125                                                                     TAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAA                                                                      <  6:110509/149‑1                                                                       AATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACT                                                                    <  6:90846/149‑1                                                                        ATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                              >  4:289/1‑138                                                                        ATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGA                                                                              <  3:289/138‑1                                                                                TTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGC                                                           >  2:57453/1‑149                                                                                     TGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACA                                                      <  3:47161/149‑1                                                                                     TGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACA                                                      <  3:35432/149‑1                                                                                          TACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTG                                                                                                        >  6:83728/1‑94                                                                                          TACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTG                                                                                                        <  5:83728/94‑1                                                                                                    GCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTT                                                                                      >  1:130370/1‑102                                                                                                    GCTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTT                                                                                      <  2:130370/102‑1                                                                                                     CTATTTTTAAACAGACACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGT                                        >  5:100082/1‑147                                                                                                                     ACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAG                       >  2:119295/1‑148                                                                                                                     ACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATC                                                                                                          <  4:89028/65‑1                                                                                                                     ACTTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATC                                                                                                          >  3:89028/1‑65                                                                                                                       TTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCA                                          >  2:29913/1‑127                                                                                                                       TTACCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCA                                          <  1:29913/127‑1                                                                                                                          CCGCACAACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAA                   >  2:129591/1‑147                                                                                                                                AACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGT                               >  4:27015/1‑129                                                                                                                                AACAAACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGT                               <  3:27015/129‑1                                                                                                                                     ACTAAGGAAGGTGTGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT      >  3:107249/1‑149                                                                                                                                     ACTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGT      <  1:119295/149‑1                                                                                                                                      CTAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTC     >  2:154034/1‑149                                                                                                                                       TAAGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTAATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCC    >  5:77052/1‑149                                                                                                                                         AGGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  >  2:102825/1‑149                                                                                                                                                                                                                                                                                               AAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATAACTCACCGTAAATAATCATCTGCTATAAATAATCACTTTCATGCAATACCAGATAAGCTATTTTTAAACAGACACTTACCGCACAACAAACTAA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/1979353‑1979489 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑GGAAGGTGCGAACAAGTCCCTGATATGAGATCATGTTTGTCATCTGGAGCCATAGAACAGGGTTCATCATGAGTCATCAACTTACCTTCGCCGACAGTGAATTCAGCAGTAAGCGCCGTCAGACCAGAAAAGAGATTTTCTTGTCCCG  <  NC_000913/2290113‑2289966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ 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.