Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	USA300TCH1516_ALE	1,441,102	(TGTTG)1→2	coding (127/624 nt)	USA300HOU_RS07160 →	hypothetical protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	= 1441097	0 (0.000)	36 (1.040) +TGTTG	16/274	0.6	100%	coding (122/624 nt)	USA300HOU_RS07160	hypothetical protein
	?	USA300TCH1516_ALE	1441098 =	0 (0.000)					coding (123/624 nt)	USA300HOU_RS07160	hypothetical protein

AAAGGAAGATGACAGTGAGATATAATATTTCTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTTAGAGGTATTTTAAA  >  USA300TCH1516_ALE/1440962‑1441241                                                                                                                                         |                                                                                                                                                aagatgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCttttt                                                                                                                                      <  2:289456‑M2/12‑1 (MQ=255) aagatgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCttttt                                                                                                                                      <  2:380400‑M2/12‑1 (MQ=255)    atgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAAt                                                                                                                                   <  2:245166‑M2/15‑1 (MQ=255)    atgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAAt                                                                                                                                   <  2:220428‑M2/15‑1 (MQ=255)    atgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAAt                                                                                                                                   <  2:350660‑M2/15‑1 (MQ=255)    atgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAAt                                                                                                                                   <  1:352619‑M2/15‑1 (MQ=255)     tgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATg                                                                                                                                  >  2:297072‑M2/133‑148 (MQ=255)     tgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATg                                                                                                                                  >  2:190046‑M2/133‑148 (MQ=255)     tgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATg                                                                                                                                  >  1:200265‑M2/133‑148 (MQ=255)     tgacagtgagatataatatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATg                                                                                                                                  >  1:130322‑M2/133‑148 (MQ=255)                     tatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATAc                                                                                                                  <  1:345780‑M2/32‑1 (MQ=255)                     tatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATAc                                                                                                                  >  2:307022‑M2/117‑148 (MQ=255)                     tatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATAc                                                                                                                  >  2:83024‑M2/117‑148 (MQ=255)                     tatttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattggtgTGTTGGCTTTTTAATGACATACCTACCGATAc                                                                                                                  >  1:381971‑M2/117‑148 (MQ=255)                      atttctcatatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatctttgttaattgatatgtcgattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACa                                                                                                                 >  1:390817‑M2/116‑148 (MQ=255)                            catatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACt                                                                                                           <  1:369661‑M2/39‑1 (MQ=255)                            catatatttggggtgttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACt                                                                                                           <  2:154649‑M2/39‑1 (MQ=255)                                          gttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAat                                                                                             >  1:234488‑M2/96‑148 (MQ=255)                                          gttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAat                                                                                             >  1:30396‑M2/96‑148 (MQ=255)                                          gttagtgggaattcctgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAat                                                                                             <  1:228647‑M2/53‑1 (MQ=255)                                                         tgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTg                                                                              <  1:205592‑M2/68‑1 (MQ=255)                                                         tgtagcgtttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTg                                                                              <  1:144507‑M2/68‑1 (MQ=255)                                                         tatagcatttttaacaagcatatttgtgattattgcacgtgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATAAAAAAAAAAAAAAAAACTCACTTCACGCAAATATTTAAACGAAATTg                                                                              <  2:300862‑M2/68‑1 (MQ=255)                                                                 ttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACt                                                                      >  1:279907‑M2/73‑148 (MQ=255)                                                                 ttttaacaagcatatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACt                                                                      >  1:159233‑M2/73‑148 (MQ=255)                                                                            atatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTa                                                           >  1:107236‑M2/62‑148 (MQ=255)                                                                            atatttgggatgattgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTGGGCTGTTTAATTACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTa                                                           >  1:370151‑M2/62‑148 (MQ=255)                                                                                         ttgcacttgatgtatcttttttatttgatttttctattggtagtggtgTGGTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACTAAATTGGTTTGACTAGAAAAGACTATCTCTATATTCGa                                              >  2:370128‑M2/49‑148 (MQ=255)                                                                                         ttgcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTAAATTAACGAAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGa                                              >  1:102472‑M2/49‑148 (MQ=255)                                                                                         ttgcacttgatgtatcttttttaattgatatgtctattggnattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATGGCTATATTCGa                                              >  1:319468‑M2/49‑148 (MQ=255)                                                                                           gcacttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTTATTTCTTACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGaaa                                            >  2:33401‑M2/47‑148 (MQ=255)                                                                                               ttgatgtatcttttttaattgatatgtctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAg                                        >  2:167914‑M2/43‑148 (MQ=255)                                                                                                                          ctattggtattgttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACCTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACCTaga             >  2:86232‑M2/16‑148 (MQ=255)                                                                                                                                     tttgTGTTGGCTTTTTAATGACATAACTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTTAGAGGTATTTTaaa  <  2:290736‑M2/144‑1 (MQ=255)                                                                                                                                     gttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTTAGAGGTATTTTaaa  <  2:70424‑M2/144‑1 (MQ=255)                                                                                                                                     gttgTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTTAGAGGTATTTTaaa  <  2:87049‑M2/144‑1 (MQ=255)                                                                                                                                         |                                                                                                                                                AAAGGAAGATGACAGTGAGATATAATATTTCTCATATATTTGGGGTGTTAGTGGGAATTCCTGTAGCGTTTTTAACAAGCATATTTGGGATGATTGCACTTGATGTATCTTTTTTAATTGATATGTCTATTGGTATTGTTGGCTTTTTAATGACATACCTACCGATACAAAAACTCACTTCACGCAAATATTTAAACGAAATTGGTTTGACTAGAAAAGACTATCGCTATATTCGAAATCAGTTAAATCATACACACCAAAAACTTAGAGGTATTTTAAA  >  USA300TCH1516_ALE/1440962‑1441241

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