Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	643,716	Δ21 bp	7.4%	intergenic (‑364/+165)	yjjP_1 ← / ← USA300HOU_RS03070	Inner membrane protein YjjP/Putative heme‑dependent peroxidase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 643715	40 (0.630)	3 (0.050)	3/254	NT	7.4%	intergenic (‑363/+186)	yjjP_1/USA300HOU_RS03070	Inner membrane protein YjjP/Putative heme‑dependent peroxidase
	?	USA300TCH1516_ALE	643737 =	36 (0.580)					intergenic (‑385/+164)	yjjP_1/USA300HOU_RS03070	Inner membrane protein YjjP/Putative heme‑dependent peroxidase

ATAGGTTAAAATAATATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGAAAAATTCCAAGCTTAAACC  >  USA300TCH1516_ALE/643575‑643855                                                                                                                                             |                                                                                                                                             aTAGGTTAAAATAATATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTAT                                                                                                                                              <  1:665100‑M1/141‑1 (MQ=255)  taGGTTAAAATAATATTAGTTAACTATTACAAAAATTGGATAGAGTAGCGACTGTATAATTTCTATTGATGTTAACGGTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATg                                                                                                                                             <  2:345060/141‑1 (MQ=255)  taGGTTAAAATAATATTAGTTAAATATTAAAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTTGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATg                                                                                                                                             <  2:694121/141‑1 (MQ=255)   aGGTTAAAATAATATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATtg                                                                                                                                            <  1:319429‑M1/141‑3 (MQ=255)     gTTAAAATAATATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGc                                                                                                                                          <  1:596522/141‑1 (MQ=255)      ttAAAAGAATAATAGTAAAAAAATACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCa                                                                                                                                         <  2:59325/141‑1 (MQ=255)        aaaaTAATATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCaaa                                                                                                                                       >  1:480348/1‑141 (MQ=255)          aataatATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGACAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAgt                                                                                                                                     <  2:11372/141‑1 (MQ=255)          aataagATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAgt                                                                                                                                     <  2:20473/141‑1 (MQ=255)             aataTTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTa                                                                                                                                  >  1:160700/1‑141 (MQ=255)              atatTAGTTAACCATTACAAAAATTGTGTAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTAc                                                                                                                                 >  1:228064/1‑141 (MQ=255)                atTAGTTAACCATTACAAAAATTGTATAGAGTAGCGAATGTATAATTTCTATTGAGGTTAACGTTTATATCCAGTGATAGTAGTTAAAGTTCTCCCAACGAAGACTACTCGCGTACACTTTGCTATtgctactccattagc                                                                                                                               >  2:200682‑M1/1‑126 (MQ=255)                            ttACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGataa                                                                                                                   <  1:592606/141‑1 (MQ=255)                              aCAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGataata                                                                                                                 <  1:24715/141‑1 (MQ=255)                               cAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATAc                                                                                                                <  2:80795/141‑1 (MQ=255)                                   aaTTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCAGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTa                                                                                                            >  2:294027/1‑141 (MQ=255)                                      tGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTGCTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGca                                                                                                         <  1:397471/141‑1 (MQ=255)                                               tAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACatatatat                                                                                                <  2:32286/141‑1 (MQ=255)                                                   gACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATGTATAAGt                                                                                            <  1:96370/141‑1 (MQ=255)                                                              ttCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACa                                                                                 <  1:668940/141‑1 (MQ=255)                                                                    tGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTc                                                                           <  1:485613/141‑1 (MQ=255)                                                                               tttATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTAcc                                                                <  1:118361/141‑1 (MQ=255)                                                                               tttATATGTAGTGATAGTAGTTAAAGTTCGTACAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTAcc                                                                <  2:686351/141‑1 (MQ=255)                                                                                tgatatGTAGTGATAGTAGTTAAAGTATTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCa                                                               <  2:623617/139‑1 (MQ=255)                                                                                 tataTGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCaa                                                              <  1:215993/141‑1 (MQ=255)                                                                                  atatGTAGTGATAGTAGTTTAAGGTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTGAAACATACAGATTTCAACTATTTACCaaa                                                             <  2:735/141‑1 (MQ=255)                                                                                  atatGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCaaa                                                             >  1:347243/1‑141 (MQ=255)                                                                                   tatGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATtgataatacattagcacatatatataagtttaaacatacagatttcaactatttaccaaatcacgtcttatgtatacgggaa                                                            <  1:730316‑M1/141‑83 (MQ=255)                                                                                    atGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATc                                                           <  1:47603/141‑1 (MQ=255)                                                                                    atGGAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATACTACATTAGCACATATATATCAGTTTAAACATACAGATTTCAACTATTTACCAAATc                                                           <  1:113738/141‑1 (MQ=255)                                                                                     tGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCa                                                          <  1:33604/141‑1 (MQ=255)                                                                                     ggTACTGATGGTAGTTAATGGTCTCCGAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATTCAGATTTCAACTATTTACCAAATCa                                                          <  2:42253/140‑1 (MQ=255)                                                                                       tAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACg                                                        >  2:295898/1‑141 (MQ=255)                                                                                        aGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACAAAATCACGt                                                       >  2:446896/1‑141 (MQ=255)                                                                                         ttgATAGTAGTTAAAGTTCTCCCAAGGAGGACTACTCGGGTACACTTTGCTATtgataatacattagcacatatatataagtttaaacatacagatttcaactatttaccaaatcacgtcttatgtatacgggaatatact                                                      <  1:528326‑M1/140‑89 (MQ=255)                                                                                              agtagtTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATg                                                 >  1:544960/1‑141 (MQ=255)                                                                                                  gtTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATATCCACTATTTACTAAATCACGTCTtatatata                                             >  2:104106/1‑141 (MQ=255)                                                                                                   ttAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATCTATAc                                            >  2:289649/1‑141 (MQ=255)                                                                                                       aGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTAGTTTGTGATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGa                                        <  2:276352/141‑1 (MQ=255)                                                                                                               cAAGGAAGACCACTCGGGTACCCTATGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTg                                <  1:603572/141‑1 (MQ=255)                                                                                                                 aGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGaa                              >  1:502427/1‑141 (MQ=255)                                                                                                                   gAAGACTACTCAAATACATTTTGCTATGCGCAAAGTATACTTTGTTATTGATAATACATTAGTCCTTATATATAAGTTTAAACATATAGATTTCCACTATTTACCAAATCCTGTCTTATGTATACTGGCACATACTGaaca                            >  2:762164/1‑139 (MQ=255)                                                                                                                       actactCGGGTACACGTTGCTATGAGCAAAGTGTAATTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATaaa                        <  2:748770/141‑1 (MQ=255)                                                                                                                           ctCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATTTATACGCGAATATACTAAAGATAAACGaa                    >  2:224364/1‑141 (MQ=255)                                                                                                                               ggTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGAAAAAt                <  1:764351/141‑1 (MQ=255)                                                                                                                                  acacTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTCTTTACAAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACCCAAAATTcc             >  2:23859/1‑141 (MQ=255)                                                                                                                                  acacTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGAAAAATTcc             >  1:419942/1‑141 (MQ=255)                                                                                                                                   cacTTTGCTATGAGCAAAGTATACTCTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTGCAACTATTTACCAAATCACGGCTTATGTATACGGGAATATCCTGAAGATAAACAAAAGAttata            >  2:709338/1‑138 (MQ=255)                                                                                                                                    acTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGAAAAATTCCaa           >  1:434658/1‑141 (MQ=255)                                                                                                                                            aTtgataatacattagcacatatatataagtttaaacatacagatttcaactatttaccaaatcacgtcttatgtatacgggaatatactgaagataaacgaaaaattccaagcttaaaccgataagcttggacttttttt   >  2:40772‑M1/1‑2 (MQ=255)                                                                                                                                            aTtgataatacattagcacatatatataagtttaaacatacagatttcaactatttaccaaatcacgtcttatgtatacgggaatatactgaagataaacgaaaaattccaagcttaaaccgataagcttggaattttttt   >  1:28660‑M1/1‑2 (MQ=255)                                                                                                                                             tGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGAAAAATTCCAAGCTTAAAcc  <  1:750529/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                             ATAGGTTAAAATAATATTAGTTAACCATTACAAAAATTGTATAGAGTAGCGACTGTATAATTTCTATTGAGGTTAACGTTTATATGTAGTGATAGTAGTTAAAGTTCTCCCAAGGAAGACTACTCGGGTACACTTTGCTATGAGCAAAGTGTACTTTGTTATTGATAATACATTAGCACATATATATAAGTTTAAACATACAGATTTCAACTATTTACCAAATCACGTCTTATGTATACGGGAATATACTGAAGATAAACGAAAAATTCCAAGCTTAAACC  >  USA300TCH1516_ALE/643575‑643855

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ 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.