Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	CP009273	2,400,257	IS5 (+) +4 bp	intergenic (‑137/‑780)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP009273	2282398 =	NA (NA)	48 (1.130)	33/296	0.3	100%	noncoding (1195/1195 nt)	IS5	repeat region
	?	CP009273	2400257 =	0 (0.000)					intergenic (‑137/‑783)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
*	?	CP009273	= 2283592	NA (NA)	35 (0.820)	29/296	0.5	100%	noncoding (1/1195 nt)	IS5	repeat region
	?	CP009273	= 2400260	0 (0.000)					intergenic (‑140/‑780)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2

AAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/2282545‑2282398 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTC  >  CP009273/2400257‑2400397                                                                                                                                                                                                                                                                                                   AAAAACGTGGGATAACCCCTGAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCC                                                                                                                                              <  1:3401/149‑1  AAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCT                                                                                                                                             >  2:29989/1‑149  AAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCT                                                                                                                                             >  1:673689/1‑149  AAAACTGGGGATAACGACTTAAATGGCGAGGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAACGGACTGAGTCAGCCGAGAAGAATTTCGCCGATGATTCGCGACTTCCCT                                                                                                                                             >  1:436718/1‑149  AAAACTGGCGATACCGCCTTAAAGGGCGAAGAAACGGTCGAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCT                                                                                                                                             <  1:380863/149‑1   AAACTGGGGATAACGCCTTAAATGGGGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTA                                                                                                                                            >  1:346417/1‑149    AACTGGGGATAACGGCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAA                                                                                                                                           <  2:117837/149‑1    AACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAA                                                                                                                                           <  1:80926/149‑1     cCTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAA                                                                                                                                          <  2:271113/148‑1     ACTGGGGTTAACGGCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAAGCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAACTTCCCCGCTTATTCGCACCTTCCCTAAA                                                                                                                                          <  2:416417/149‑1     ACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACGTGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAcc                                                                                                                                          >  2:27246/1‑147     ACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAA                                                                                                                                          <  2:616864/149‑1     ACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAA                                                                                                                                          >  2:572917/1‑149        GGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAA                                                                                                                                       <  2:657081/149‑1          GGATAACGCCTTAAATGGCGAAGAAAGGGTCTTTTTAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGC                                                                                                                                     >  1:339120/1‑149                 GCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGCATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCAC                                                                                                                              >  2:223290/1‑149                 GCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCAC                                                                                                                              >  1:191461/1‑149                   CTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCGCAT                                                                                                                            >  1:576219/1‑149                    ttcAATGGCGAAGAAACGGTCTAAAGAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATT                                                                                                                           <  2:695188/146‑1                            CGAAGAAACGGTCTAAATCGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTT                                                                                                                   >  1:510822/1‑149                             GAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTA                                                                                                                  <  1:535172/149‑1                                   ACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGC                                                                                                            <  1:645490/149‑1                                     GGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCT                                                                                                          <  1:381190/149‑1                                               GGCTGATTCAAGTCATTTACGAGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATC                                                                                                <  1:33035/149‑1                                                  TGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACA                                                                                             <  1:594251/149‑1                                                          GGCATTTACGGGAGAAAAAATAGGCACAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATAT                                                                                     <  2:366525/149‑1                                                                TACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTCCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAG                                                                               <  2:317620/149‑1                                                                        AAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGGTATACTGCCGGAAGTAGATCACAGAATATATGTTAAGGGGTCGCA                                                                       >  1:118314/1‑149                                                                           AAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATAT                                                                    <  1:522888/149‑1                                                                               CGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTAT                                                                <  2:230650/149‑1                                                                                    CAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGT                                                           <  1:84732/149‑1                                                                                     AAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCTTATCTATTAAGTT                                                          >  2:220238/1‑149                                                                                                AATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTAACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTT                                               >  1:103057/1‑149                                                                                                 ATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTT                                              >  1:403045/1‑149                                                                                                  TGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTC                                             >  2:190726/1‑149                                                                                                             AGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGGTCCGTTATAATGCCTAAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTAACTCTTTTCTATTTATGACA                                  >  2:383666/1‑149                                                                                                              GTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACAT                                 <  2:510822/149‑1                                                                                                               TCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATG                                >  1:518331/1‑149                                                                                                                      AGAAGAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATACATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGT                         <  2:426116/149‑1                                                                                                                        AAGATTTCCCCCGCTTATTCGCACCTTCCCAAAAAAAGCGACCCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTT                       <  1:64685/149‑1                                                                                                                          GAATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGGTCACAGAATATATCTGCAGGGATCGGATATCTATTAAGTTTCTCCCTCTTTTCTTTTTATGACATGTGCGTGGTTGT                     >  2:346933/1‑149                                                                                                                           AATTTCCCCGCTTATTCGCACCTTCCCTACACAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTA                    <  1:572917/149‑1                                                                                                                           AATTTCCCCGCTTATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATAGCTTCAGGGATCGCATATCTATTCAGTTACTCACTCTTTTCTATTTCTGACATGCGGTTGTTTGTc                    >  2:95190/1‑148                                                                                                                             TTTCCCCTCTTATTCGCACCTTCCCTAAAAAAGCGACCCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATA                  <  2:576219/149‑1                                                                                                                                CCCCGTCTAGTCGCACCTCCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGTGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAAT               <  2:366651/149‑1                                                                                                                                      ttcTTCGCATCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAAT         <  2:652295/146‑1                                                                                                                                        ATTCGCACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGT       >  2:675466/1‑149                                                                                                                                             CACCTTCCCTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTC  >  2:120947/1‑149                                                                                                                                                                                                                                                                                                   AAAAACTGGGGATAACGCCTTAAATGGCGAAGAAACGGTCTAAATAGGCTGATTCAAGGCATTTACGGGAGAAAAAATCGGCTCAAACATGAAGAAATGAAATGACTGAGTCAGCCGAGAAGAATTTCCCCGCTTATTCGCACCTTCC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  CP009273/2282545‑2282398 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑CTAAAAAAGCGACTCACATTGTTCCGTTATAATGCCTGAAGTAGATCACAGAATATATCTTCAGGGATCGCATATCTATTAAGTTACTCACTCTTTTCTATTTATGACATGCGCGTGTTTGTATAAATGTAAATGTGAGTC  >  CP009273/2400257‑2400397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ 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.