Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC JC	NC_000913	1,979,486	IS5 (+) +4 bp	intergenic (‑271/‑264)	insA ← / → uspC	IS1 repressor TnpA/universal stress protein

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	1979486 =	0 (0.000)	69 (1.520)	45/282	0.1	100%	intergenic (‑271/‑267)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	2101749 =	NA (NA)					noncoding (1195/1195 nt)	IS5	repeat region
*	?	NC_000913	= 1979489	0 (0.000)	63 (1.390)	44/282	0.1	100%	intergenic (‑274/‑264)	insA/uspC	IS1 repressor TnpA/universal stress protein
	?	NC_000913	= 2290113	NA (NA)					noncoding (1/1195 nt)	IS5	repeat region

TCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGA  >  NC_000913/2289981‑2290255                                                                                                                                     |                                                                                                                                                tctTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGt                                                                                                                                       >  2:66858/1‑143 (MQ=37)   ttttCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAg                                                                                                                                     >  2:596017/1‑143 (MQ=38)           tCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATCTCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGa                                                                                                                             >  1:549254/1‑143 (MQ=255)           tCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTAATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGa                                                                                                                             >  1:675952/1‑143 (MQ=255)            cTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGaa                                                                                                                            >  1:266994/1‑143 (MQ=255)            cTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCACGGACTTGTTCGCACCTTCCATAACGATGTCAccaccaaga                                                                                                                            >  2:421291/1‑140 (MQ=11)             tGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACGCTGTTCTATGGCCCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCCCCTTCCATAAGCCTGTAGCCACCAGAAc                                                                                                                           >  2:499226/1‑143 (MQ=14)             tGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACACTGTAGCAACCAGAAc                                                                                                                           >  1:324523/1‑143 (MQ=255)                         ctgctgAATGCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGa                                                                                                               <  1:235677/143‑1 (MQ=255)                          tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGCATTGTTCGACCCTTCCATAACGCTGTAGCACCCACAACAGATATTGCGGaa                                                                                                              >  2:385603/1‑143 (MQ=17)                            ctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGCACAGATATTGCGGAACg                                                                                                            >  1:704155/1‑143 (MQ=255)                                       gTCGGCGAAGGTAAGCTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCGCCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGaaa                                                                                                <  2:346384/143‑1 (MQ=255)                                           gCGACGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACACACACGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGa                                                                                            <  1:431222/143‑1 (MQ=255)                                                      ttGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGAt                                                                                 >  1:557636/1‑143 (MQ=255)                                                           gaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGTCTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATCTT‑AGTAGTGTACAATGAGATACAGAACCAGATTGATGCAtt                                                                            >  1:344355/1‑143 (MQ=18)                                                            aCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATATAATATCAGGGACTTGTTCGCACCTTACATAACGCTGTAGCAACAAGAAAAGATATTGTGGAACG‑ACAAAGAGAAACAGAAAAAGATTGATGAATTg                                                                           >  2:302202/1‑143 (MQ=21)                                                              tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATCGCGGAACG‑ACCCAGAGAAACAGAACCAGATTGATGCCTTgcg                                                                         >  2:522143/1‑141 (MQ=255)                                                              tCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATACTGCGGAACG‑ACCAAGAGAAAGCGAACCAGAGTGCTGCATCGAg                                                                         >  2:51386/1‑143 (MQ=21)                                                                aggatgaCCCCTGTTCTATGGCTCCTGAGGATAAACTTGATCTCATAGCATGGACTTGTTCGCACCTTGCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCt                                                                       <  2:285249/141‑1 (MQ=255)                                                                  gatgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACTCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCttt                                                                     >  2:624542/1‑143 (MQ=255)                                                                   atgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTc                                                                    <  2:824259/143‑1 (MQ=255)                                                                   atgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCCCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGCTATTGCGGAACG‑ACAAAGAGAAACAGAACCAGAATGATGCATTCAGGTTTc                                                                    >  2:518786/1‑143 (MQ=25)                                                                      gaCCCGGTCCTATTGCGCCAGCGGACAAACATGACGTCATATCAGGGACTTGTGCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATAGTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGAGGCATTGAGCTTTCATc                                                                 <  2:692272/142‑1 (MQ=255)                                                                      aaCCCTGTTCTATGGCTCCAGATGACAACCATGATCTCATATCAGGCACTTGCTCGCACCTTCCATAACGCTGTAGCCACCACAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATc                                                                 <  1:719769/143‑1 (MQ=255)                                                                      aaCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTGAtg                                                                 >  2:49624/1‑142 (MQ=255)                                                                        cccTGTTCTATGGCTCCAGATGACAAACATGCTCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGCGAAACCGAACCAGATTGACGCATTGAGCTTTCATCCt                                                               >  2:64784/1‑143 (MQ=255)                                                                         ccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTa                                                              >  1:138048/1‑143 (MQ=255)                                                                          cTGTTCGATGGCTCNAGATGACAAACATGATCTCATATCAGGGACTTGGTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGNTATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTNTCATCCTAt                                                             <  1:713536/143‑1 (MQ=255)                                                                           tGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATg                                                            >  2:279935/1‑143 (MQ=255)                                                                              tcgaTGGGTCCGGATGACAAACATGATCGCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGaaa                                                         <  2:141631/140‑1 (MQ=255)                                                                              tCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCCGTAGTCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGaag                                                         >  1:101497/1‑142 (MQ=255)                                                                              gcgctGGCTCCAGAGGACAAACATGATCTCATATCAGGGACTTGTTTGCACCGTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGTTTGATGCAGTGAGCTTTCATCCTATGaaa                                                         <  2:141289/139‑1 (MQ=38)                                                                                    gCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACGAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAaattaatt                                                   >  2:228947/1‑143 (MQ=255)                                                                                      tCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATACCGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAGACAGAACCAGATTGATGCATTCACCTTTCATCCTATGAAAATAATTGc                                                 >  2:117367/1‑143 (MQ=38)                                                                                         aggtGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGt                                              <  2:319426/140‑1 (MQ=255)                                                                                         aGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGACACGAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATGGATGCATTGAGCTTTCGTCCTATGGAATTAACTGcggc                                              >  1:313754/1‑140 (MQ=37)                                                                                           aTGAAAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTa                                            <  1:698/143‑1 (MQ=255)                                                                                                 aaCATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCa                                      >  1:288966/1‑143 (MQ=255)                                                                                                       aTCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAACTTAATTGCTGTTAAAAGCATTgggg                                >  1:94961/1‑142 (MQ=255)                                                                                                       aTCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGt                                >  2:222477/1‑143 (MQ=255)                                                                                                        tctcATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTa                               >  1:686222/1‑143 (MQ=255)                                                                                                            atatCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGa                           <  1:645296/143‑1 (MQ=255)                                                                                                               tCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGaaaa                        >  1:572527/1‑143 (MQ=255)                                                                                                                  gtgACTTGTTTGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATAc                     <  2:555712/141‑1 (MQ=255)                                                                                                                        tGTTCGCACCTGCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACACAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCAtcg               >  2:336574/1‑141 (MQ=255)                                                                                                                             gCACCTTGCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCa          <  1:119265/143‑1 (MQ=255)                                                                                                                             gCACCTTCCATAACGCTGTAGCCACCCCTACATGTTGGTCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCa          <  1:221288/143‑1 (MQ=255)                                                                                                                             gCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAACGCATTGGGTACAGAAAATACCCATAGCTCCa          >  1:640752/1‑143 (MQ=255)                                                                                                                             gCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCa          >  2:787841/1‑143 (MQ=255)                                                                                                                                     cATAGCGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGa  <  1:66858/143‑1 (MQ=255)                                                                                                                                     |                                                                                                                                                TCTTTTCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCATAACGCTGTAGCCACCAGAACAGATATTGCGGAACG‑ACAAAGAGAAACAGAACCAGATTGATGCATTGAGCTTTCATCCTATGAAATTAATTGCTGTTAAAAGCATTGGGTACAGAAAATACCCATAGCTCCATACCCGGA  >  NC_000913/2289981‑2290255

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ 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.