Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	998,719	IS2 (–) +5 bp	coding (230‑234/702 nt)	elfD →	putative periplasmic pilin chaperone

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	381260 =	NA (NA)	63 (1.240)	57/298	0.0	100%	noncoding (1/1331 nt)	IS2	repeat region
	?	NC_000913	998719 =	0 (0.000)					coding (230/702 nt)	elfD	putative periplasmic pilin chaperone
*	?	NC_000913	= 998723	0 (0.000)	51 (1.000)	43/298	0.3	100%	coding (234/702 nt)	elfD	putative periplasmic pilin chaperone
	?	NC_000913	1467910 =	NA (NA)					noncoding (1331/1331 nt)	IS2	repeat region

AAAGGCGGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/998574‑998723 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCT  >  NC_000913/1467910‑1468059                                                                                                                                                                                                                                                                                                              AAAGGCGGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTT                                                                                                                                                       >  1:722676/1‑151  AAGGCGGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTG                                                                                                                                                      <  2:174078/151‑1  AAGGCGGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTG                                                                                                                                                      >  1:402748/1‑151   AGGCGGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGG                                                                                                                                                     <  2:668322/151‑1     GCGGGATTGTACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGAT                                                                                                                                                   >  1:610913/1‑151       GGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTT                                                                                                                                                 <  1:252315/151‑1            TGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCC                                                                                                                                             <  2:641856/150‑1             GGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCT                                                                                                                                           <  2:599442/151‑1                 TTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATAT                                                                                                                                       >  1:40140/1‑151                    CAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTC                                                                                                                                    <  2:651785/151‑1                          CACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGAC                                                                                                                               >  1:639374/1‑150                            CGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATC                                                                                                                            <  1:241549/151‑1                             GTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCT                                                                                                                           <  1:638016/151‑1                                TTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTT                                                                                                                        >  1:656047/1‑151                                TTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTT                                                                                                                        >  2:359130/1‑151                                 TGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCT                                                                                                                                           <  1:548189/131‑1                                 TGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCT                                                                                                                                           >  2:548238/1‑131                                     TATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCA                                                                                                                    <  1:310749/150‑1                                     TATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCA                                                                                                                    <  1:66664/150‑1                                       TTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTT                                                                                                                 >  2:790854/1‑151                                         CAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAA                                                                                                               <  2:335429/151‑1                                            AAGGTGAAGAGCAAATTTCACTGGGTGAACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCC                                                                                                            >  1:407529/1‑151                                                   AGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAA                                                                                                     <  2:157452/151‑1                                                      GCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCC                                                                                                  <  1:190106/151‑1                                                         AATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGC                                                                                               >  2:262865/1‑151                                                              aACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCG                                                                                          >  1:191683/2‑151                                                                  GGGTGTACGTAACACCGGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCg                                                                                        <  1:520786/149‑2                                                                    GTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATA                                                                                    <  2:29904/151‑1                                                                      GTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATT                                                                                  <  2:92870/151‑1                                                                         CGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCC                                                                               <  1:706923/151‑1                                                                               ACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCG                                                                         <  1:52890/151‑1                                                                                      CGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATA                                                                  <  2:171383/151‑1                                                                                           GTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCA                                                             <  2:788779/151‑1                                                                                           GTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCC                                                              >  2:217993/1‑150                                                                                                 TATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGC                                                         <  1:575776/149‑1                                                                                                     TTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATG                                                   >  2:529339/1‑151                                                                                                      TATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACT                                                      <  2:407588/147‑1                                                                                                           AGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATG                                             >  1:613400/1‑151                                                                                                                   GTGATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGT                                     <  1:113643/151‑1                                                                                                                     GATGACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTT                                    <  2:172819/150‑1                                                                                                                        GACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAA                                <  1:461279/151‑1                                                                                                                        GACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAA                                <  1:458553/151‑1                                                                                                                        GACCCCAGATAATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATA                                 >  1:601788/1‑150                                                                                                                                  AATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACG                      >  1:140802/1‑151                                                                                                                                  AATAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAA                        >  1:549062/1‑149                                                                                                                                    TAAAAAATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCC                    >  1:772683/1‑151                                                                                                                                         AATCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGC               <  2:613455/151‑1                                                                                                                                           TCAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCA              >  2:747369/1‑150                                                                                                                                            CAGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCA              >  2:550562/1‑149                                                                                                                                             AGCAGACTTTTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGG           >  2:75295/1‑151                                                                                                                                                      TTGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCT  >  2:42658/1‑151                                                                                                                                                                                                                                                                                                              AAAGGCGGGATTGGACTTGCAGCAACACGTCTTGTTTATTCAGAAGGTGAAGAGCAAATTTCACTGGGTGTACGTAACACCAGTCCGGATGTTCCTTATCTTATTCAGTCATGGGTGATGACCCCAGATAATAAAAAATCAGCAGACTTT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  NC_000913/998574‑998723 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TGGATTTGCCCCTATATTTCCAGACATCTGTTATCACTTAACCCATTACAAGCCCGCTGCCGCAGATATTCCCGTGGCGAGCGATAACCCAGCGCACTATGCGGATGCCATTCGTTATAATGCTCGAACGCCTCTGCAAGGTTCTTTGCT  >  NC_000913/1467910‑1468059

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ 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.