Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC JC	CP009273	1,427,903	IS3 (–) +3 bp	15.1%	coding (27‑29/591 nt)	pinR ←	Rac prophage; putative site‑specific recombinase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	1089701 =	NA (NA)	24 (0.110)	18/276	NT	NA	noncoding (1258/1258 nt)	IS3	repeat region
	?	CP009273	= 1427905	NA (NA)					coding (27/591 nt)	pinR	Rac prophage; putative site‑specific recombinase
*	?	CP009273	= 1090958	NA (NA)	26 (0.120)	21/276	NT	14.8%	noncoding (1/1258 nt)	IS3	repeat region
	?	CP009273	1427903 =	146 (0.660)					coding (29/591 nt)	pinR	Rac prophage; putative site‑specific recombinase

AGCAAGCTTCAGGGCTTCACTGCGAAATTCAGGCGAATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/1090813‑1090958 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGC  >  CP009273/1427903‑1428045                                                                                                                                                                                                                                                                                                   AGCAAGCTTCAGGGCTTCACTGCGAAATTCAGGCGAATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATC                                                                                                                                              >  2:3157292/1‑149                        GAAATTCAGGCGAATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGA                                                                                                                       >  1:3632854/1‑149                           ATTCAGGCGAATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACAT                                                                                                                    <  1:3880430/149‑1                               AGGCGAATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTG                                                                                                                <  1:3018812/149‑1                                    AATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACT                                                                                                           >  2:3322423/1‑149                                     ATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTC                                                                                                          <  2:3489187/149‑1                                            TTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGA                                                                                                   >  1:2003415/1‑149                                                            TGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATC                                                                                   <  2:3031080/149‑1                                                                   TACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGC                                                                            <  1:2086098/149‑1                                                                   TACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGC                                                                            <  1:2086649/149‑1                                                                      TGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATC                                                                         <  1:1949458/149‑1                                                                               CATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAAT                                                                >  2:3726631/1‑149                                                                               CATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAAT                                                                >  2:3726734/1‑149                                                                                ATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATA                                                               <  1:4153116/149‑1                                                                                   TGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATT                                                            <  2:1814447/149‑1                                                                                        CACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGAT                                                       <  1:4353039/149‑1                                                                                             CTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTT                                                  <  2:2051021/149‑1                                                                                             CTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTT                                                  <  2:4274194/149‑1                                                                                                                  TAGCCGCGTGTCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACA                             >  1:2491464/1‑149                                                                                                                            TCCACTATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAA                   <  2:4116450/149‑1                                                                                                                                 TATTGCTGGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAAC              <  1:176356/149‑1                                                                                                                                        GGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCG       >  1:2755789/1‑149                                                                                                                                        GGGTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCG       >  1:2755684/1‑149                                                                                                                                          GTAAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTA     <  1:1823413/149‑1                                                                                                                                            AAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAATTTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATG   <  1:1884596/149‑1                                                                                                                                            AAGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATTATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATG   <  1:4108670/149‑1                                                                                                                                             AGATCAATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGC  >  2:2458968/1‑149                                                                                                                                                                                                                                                                                                   AGCAAGCTTCAGGGCTTCACTGCGAAATTCAGGCGAATGCTGTTTACGGGGTTTTTTACTGGTTGATACTGTTTTTGTCATGTGAGTCACCTCTGACTGAGAGTTTACTCACTTAGCCGCGTGTCCACTATTGCTGGGTAAGATCA‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP009273/1090813‑1090958 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑ATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATGC  >  CP009273/1427903‑1428045

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ 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.