Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	2,313,540	Δ2 bp :: IS186 (+) +6 bp	coding (53‑58/2673 nt)	rcsD →	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	2313540 =	0 (0.000)	53 (0.930)	42/274	0.3	100%	coding (53/2673 nt)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
	?	NC_000913	= 2515617	NA (NA)					noncoding (1345/1345 nt)	IS186	repeat region
*	?	NC_000913	= 2313545	0 (0.000)	48 (0.830)	43/278	0.3	100%	coding (58/2673 nt)	rcsD	phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
	?	NC_000913	2514275 =	NA (NA)					noncoding (3/1345 nt)	IS186	repeat region

GCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCC  >  NC_000913/2514135‑2514414                                                                                                                                             |                                                                                                                                            gCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGTTAATTCCCa                                                                                                                                           >  1:942262/1‑143 (MQ=255) gCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCa                                                                                                                                           >  1:75678/1‑143 (MQ=255)     gaatgaaGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGGAACACCACACATAAAAAAACCGGGGATAATTCCCATAAg                                                                                                                                       >  2:9200/1‑143 (MQ=255)           agagCGAGGTACCGTGGTTTCTCGTTGCGGTCTGTAGCGGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTaa                                                                                                                                 <  2:314814/143‑1 (MQ=255)                aaGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTaa                                                                                                                            <  1:531452/143‑1 (MQ=255)                aaGGTAACGCGGTTTCCCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTaa                                                                                                                            <  1:206506/143‑1 (MQ=255)                 gtgTAACGTGGTTGCTCGCTTCGGTCTGAAGCTGGGTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAg                                                                                                                           <  2:298997/141‑1 (MQ=255)                 gggTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAg                                                                                                                           <  2:107533/142‑1 (MQ=255)                  ggcaaCGTGGGTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCTCAGCACTGGTGCTGTAAGATCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAgg                                                                                                                          <  2:341450/140‑1 (MQ=255)                  ggTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAgg                                                                                                                          <  1:427116/143‑1 (MQ=255)                        gcggTGTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTCCCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCGCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTtgtg                                                                                                                    <  2:963839/141‑1 (MQ=255)                          gctttCTCGCTTCGCGCCGTAGCTGGTTTACGGCTATACCCTGGTGAGTGCGCTGTCTGCGTCAAGCGCAGCACTGGTGCTGCAAGCCCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGt                                                                                                                  <  2:143176/141‑1 (MQ=38)                               ctcGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTAc                                                                                                             >  1:196611/1‑143 (MQ=255)                                       ggTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGata                                                                                                     <  1:989980/143‑1 (MQ=255)                                          cTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGa                                                                                                  <  2:663781/143‑1 (MQ=255)                                               gCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGGGCTACCTTAAGGGTTGTGGCACTACGCCGGATATGATTTaa                                                                                             >  2:685398/1‑143 (MQ=255)                                                cTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAAc                                                                                            <  1:431495/143‑1 (MQ=255)                                                     ttACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGcc                                                                                       <  1:562886/143‑1 (MQ=255)                                                          gCTCTACCCTGGTGAGTGTGCTGTCTGCGTCCATCGCAGTGCTGGTGCTGTAAGACCATACAGAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGa                                                                                  <  1:537750/143‑1 (MQ=255)                                                          gCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGTGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGa                                                                                  <  1:565580/143‑1 (MQ=255)                                                           ctctACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGCTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGaa                                                                                 >  2:830558/1‑143 (MQ=255)                                                              tACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTa                                                                              <  1:318729/143‑1 (MQ=255)                                                                 ccTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGGCCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTCAAGGGTTGTGGTATTACGCCTGATCTGATTTAACGTGCCGATGAATTActc                                                                           >  1:1017305/1‑143 (MQ=255)                                                                   tGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACtctc                                                                         >  1:224556/1‑143 (MQ=255)                                                                   tGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGGTGTGGTATTACGCCTGATATGGTTTAACGTGCCGATGAATGACtctc                                                                         >  1:326241/1‑143 (MQ=255)                                                                        aGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGAt                                                                    <  2:75678/143‑1 (MQ=255)                                                                              cTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGCCCATACATAACAAAGCCGGGGATAGTTCCCATAAGCGCTAACTTAAGGGCTGTGCTAGTACGCCTGATATGATTTAACGTGCCGATGACTTACTCTCACGATAACTgg                                                              >  2:866407/1‑143 (MQ=21)                                                                                   tGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTCACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAgg                                                         >  1:151162/1‑142 (MQ=255)                                                                                   tGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCCCACCTAAGGGTTGTGGTATTACGCCCGATAAGATTTAACGTGCCGATCACTGACTCTCCCGACAAGCGGTAAGc                                                         >  2:880907/1‑143 (MQ=21)                                                                                     cGTCAGTCGCCGCACTTGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAATCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCaa                                                       <  2:605850/143‑1 (MQ=255)                                                                                       tCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAAtt                                                     >  1:456505/1‑143 (MQ=255)                                                                                             gcagcaCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGAATAATTCCCATAAGCGCTAACTTAAGGGTCGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACACCCACGATAACTGGTCAGCAATTCTGGca                                               >  2:767075/1‑142 (MQ=255)                                                                                               agcaCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCATGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATACTGGCCCa                                             >  1:356729/1‑143 (MQ=255)                                                                                                  aCTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCatat                                          >  2:745400/1‑143 (MQ=255)                                                                                                    tGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTg                                        >  2:728412/1‑143 (MQ=255)                                                                                                      gTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAGTTACGCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGt                                      >  1:498904/1‑143 (MQ=255)                                                                                                      gTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTAACGATAACTGGTCAGCAATTCTGGCCCATATTGGt                                      >  1:908960/1‑143 (MQ=255)                                                                                                       tGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTTGTCAGCAATTCTGGCCCgtatggcta                                     >  2:752199/1‑138 (MQ=255)                                                                                                          tGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCGATTCTGGTGCATATTGGTAAGc                                  >  1:278796/1‑143 (MQ=255)                                                                                                            tAAGACCATACATAAAAAAGCCGGGGATAGTCCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGccc                                <  2:359849/143‑1 (MQ=255)                                                                                                               gACCATACATAAAAAAGCCGGGGATACTGCCCAGAAGCGCTAACTTAAGGGGTGGGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCgaa                             <  2:102290/143‑1 (MQ=17)                                                                                                                   atacataAACAAGCCGGGGATAAGTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAAc                         <  2:203451/143‑1 (MQ=255)                                                                                                                   atacataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCACTTCTGGCCCATATAGGTAGGCCCGAAGCAc                         >  1:586951/1‑143 (MQ=255)                                                                                                                   atacataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAAc                         >  1:77744/1‑143 (MQ=255)                                                                                                                      cataAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACACCTGACAGGATTTAACGTGCCGATGAATTACTCTCACGATACCTGGTCAGCACTTCTGGCCCGTGTCGGTACGCCCGCAGAAcacg                      >  1:16726/1‑140 (MQ=14)                                                                                                                            aaaGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACtt                >  1:423434/1‑143 (MQ=40)                                                                                                                            aaaGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACtt                >  2:68532/1‑143 (MQ=39)                                                                                                                                ccGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATCTTGGTAAGCCCGAAGAACTGGATACGTCGGc            >  2:147186/1‑143 (MQ=25)                                                                                                                                    ggATAATTCCCATATGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACgg        >  1:459886/1‑142 (MQ=25)                                                                                                                                    ggATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGt        <  1:91498/143‑1 (MQ=34)                                                                                                                                          ttCCCATAAGCGCTAACTTAAGGGTCGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGcc  >  2:347405/1‑143 (MQ=11)                                                                                                                                             |                                                                                                                                            GCCTGAATGAAGAGCAAGGTAACGTGGTTTCTCGCTTCGGTCTGAAGCTGGTTTACGGCTCTACCCTGGTGAGTGTGCTGTCTGCGTCAATCGCAGCACTGGTGCTGTAAGACCATACATAAAAAAGCCGGGGATAATTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAACGTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGGATACTTCGGCACGTAATGCC  >  NC_000913/2514135‑2514414

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.