Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
JC	USA300TCH1516_ALE	1,747,374	Δ3 bp	100%	coding (2073‑2075/2280 nt)	USA300HOU_RS08710 ←	Heme uptake protein MmpL11

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	USA300TCH1516_ALE	1747377 =	1 (0.030)	23 (0.750)	20/242	NT	96.0%	coding (2072/2280 nt)	USA300HOU_RS08710	Heme uptake protein MmpL11
	?	USA300TCH1516_ALE	= 1747373	1 (0.030)					coding (2076/2280 nt)	USA300HOU_RS08710	Heme uptake protein MmpL11

GACCGTGTACGTGAAAACTTACAAAAGGTTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1747510‑1747377 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtagtagtTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTATTCTCTTCAATCTTCATTGCCGTTCCGCTATGGGGAATAATGAAAAAACGTCAGTTGAAAAAA  <  USA300TCH1516_ALE/1747373‑1747235                                                                                                                                                                                                                                                                                   tACCTTGTACGTGAAAACTTAGAAAAGGTTAAATTTATTACGACAACAGAACAAATTGATGATATGGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTAT                                                                                                                                       <  1:533970/139‑1   CCGTTTACGTGAAAACTTACAAAAGGTTAAAGTGATTACGACAAAAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATAC                                                                                                                                     <  1:580367/140‑1             GAAAACTTACAAAAGGTTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCAATACTATTCTTCGG                                                                                                                           >  1:654919/1‑140             GAAAACTTACAAAAGGTTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGAAAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGGTATACTATTCTTAGG                                                                                                                           >  1:217686/1‑140              AAAACTTAAAAAAGGTTATAGTGATTAAGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGT                                                                                                                          <  1:659422/140‑1                            GTTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACTCGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCAAAACTATTCTTCAATGCTCATACGATATT                                                                                                            >  1:307358/1‑140                            GTTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATT                                                                                                            >  1:542066/1‑140                             TTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTC                                                                                                           >  1:305618/1‑140                                      TTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACT                                                                                                  >  1:305750/1‑140                                            CAACAGAACAAATTGATTATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACATTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCA                                                                                            <  1:481864/140‑1                                                aggACAAATTGATGAAATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTAT                                                                                        <  1:125864/137‑1                                                           ATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGATGCTCCTACGATATTCAACTTTAATTTAGCAATATTTATCGGATTa                                                                             >  1:588085/1‑139                                                            TGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACCGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGATCCTAAGATATTCAACTTTACTTTAGCATTATTTATCGGATTGA                                                                            >  1:225040/1‑140                                                             GATATCGTTAATAGATCAATTCGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGACATTCAACTTTACTTTAGCATTATTTATCGGATTGAT                                                                           <  1:529385/140‑1                                                             GATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATAGGATTGAT                                                                           >  1:728589/1‑140                                                                        TAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTAT                                                                <  1:638782/140‑1                                                                         AGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCGGATTTATTTCTTGTGTATT                                                               >  1:546913/1‑140                                                                                    ACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATAGGATTGATTTCTGGTGTATTTTCTTAAATCT                                                    >  1:263335/1‑140                                                                                    ACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGAATTATTTATCAAATTGATTTCTGGTGTATTCTCTTCAATtt                                                    >  1:51010/1‑138                                                                                                ACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTATTCTCTTCAATCTTCATTGCCGTTC                                        <  1:351953/140‑1                                                                                                          AATACAGTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCGACGATATTCAACTTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTATTCTCTTCAATCTTCATTGCCGTTCCGCTATGGGG                              <  1:353746/140‑1                                                                                                                GTATTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCAGATTGATTTCTGGTGAATTCTCTTCAATCTTAATTGACGTTGCGCTAGGGGAAAAAAT                        >  1:6236/1‑140                                                                                                                   TTAACAGTTATTGTAGTAGTTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACCTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTATTCTCTTCAATCTTCATTGCCGTTCCGCTATGGGGAATAATGAA                     <  1:193814/140‑1                                                                                                                                      TTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTATTCTCTTCAATCTTCATTGCCGTTCCGCTATGGGGAATAATGAAAAAACGTCAGTTGAAAAAA  <  1:88428/140‑1                                                                                                                                                                                                                                                                                   GACCGTGTACGTGAAAACTTACAAAAGGTTAAAGTGATTACGACAACAGAACAAATTGATGATATCGTTAATAGATCAATTAGACAGACAATGACACGTTCAATTAATACAGTATTAACAGTTATTGTAGTAGT‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  <  USA300TCH1516_ALE/1747510‑1747377 ‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑gtagtagtTGCTATACTATTCTTCGGTGCTCCTACGATATTCAACTTTACTTTAGCATTATTTATCGGATTGATTTCTGGTGTATTCTCTTCAATCTTCATTGCCGTTCCGCTATGGGGAATAATGAAAAAACGTCAGTTGAAAAAA  <  USA300TCH1516_ALE/1747373‑1747235

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.