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

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	USA300TCH1516_ALE	1747374	1747376	3	30 [0]	[0] 30	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 =	0 (0.000)	25 (0.460)	21/244	NT	100%	coding (2072/2280 nt)	USA300HOU_RS08710	Heme uptake protein MmpL11
	?	USA300TCH1516_ALE	= 1747373	0 (0.000)					coding (2076/2280 nt)	USA300HOU_RS08710	Heme uptake protein MmpL11

TTTCAACTGACGTTTTTTCATTATTCCCCATAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAACTACTACTACAATAACTGTTAATACTGTATTAATTGAACGTGTCATTGTCTGTCTAATTGATCTATTAACGATATCATCAATTTGTTCTGTTGTCGTAATCACTTTAACCTTTTGTAAGTTTTCACGTACACGGTCA  >  USA300TCH1516_ALE/1747238‑1747511                                                                                                                                        |                                                                                                                                           tttCAACTGACGTTTTTTCATTATTCCCCATAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactac                                                                                                                                       <  1:446500‑M2/141‑6 (MQ=255)  ttCAACTGACGTTTTTTCATTATTCCCCATAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactact                                                                                                                                      >  1:285524‑M2/1‑135 (MQ=255)       tttatgtttttTTATTATTCCACATAGCGGAACGGCAATGAAGATTGAAGAGAATACATCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaat                                                                                                                                 >  1:201329‑M2/6‑130 (MQ=255)                tttCATTTTTCCCCATAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaa                                                                                                                        >  1:113176‑M2/1‑121 (MQ=255)                         tCCCCATAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtatt                                                                                                               <  2:172928‑M2/141‑30 (MQ=255)                             ctatgcggaACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaatt                                                                                                           >  1:596813‑M2/5‑108 (MQ=255)                              aTAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGCATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattg                                                                                                          <  2:516587‑M2/141‑35 (MQ=255)                               tAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattga                                                                                                         >  2:200453‑M2/1‑106 (MQ=255)                                 gaggaaCGGAAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGACACAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATCGTATAGCAactactacaataaacgtagatactgttataattgacc                                                                                                       <  2:182829‑M2/139‑38 (MQ=255)                                  cGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacg                                                                                                      >  2:3912‑M2/1‑103 (MQ=255)                                               aaGATTGAAGAGAATCCACCAGAACTCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgt                                                                                         >  1:279569‑M2/1‑90 (MQ=255)                                               aaGATTGAAGAGAATACACCAGAAATCTATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgt                                                                                         >  1:670412‑M2/1‑90 (MQ=255)                                                  aTTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtcta                                                                                      <  1:111405‑M2/141‑55 (MQ=255)                                                       agagATTACACCAGACATCTATCCGATAAATGGTGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattga                                                                                 >  1:94517‑M2/1‑82 (MQ=255)                                                        gagaATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctatttgat                                                                                <  2:334448‑M2/141‑61 (MQ=255)                                                        gagaATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgat                                                                                >  2:551712‑M2/1‑81 (MQ=255)                                                                      tatcaattcGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatc                                                                  >  1:148472‑M2/2‑67 (MQ=255)                                                                          aaccCGATAAATGATGCTAAGGTAAAGTGGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatca                                                              >  2:612823‑M2/1‑63 (MQ=255)                                                                             ccGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatt                                                           <  2:205768‑M2/141‑82 (MQ=255)                                                                                           taaagtaaagTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgt                                             >  1:36264‑M2/1‑46 (MQ=255)                                                                                           caaagtaaagttGAATATAGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgt                                             >  2:243787‑M2/2‑46 (MQ=255)                                                                                                        aaTATCGTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattagttgaacgtgtcattgtctgtctaattgatctattaacgatatcatcactttgttctgttgtcgtaatcactttaacc                                <  2:74348‑M2/141‑109 (MQ=255)                                                                                                             cGTAGGAGCACCGAACAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttg                           >  1:183161‑M2/1‑28 (MQ=255)                                                                                                              gTAGGAGCACCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttgt                          >  2:81061‑M2/1‑27 (MQ=255)                                                                                                                      aCCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgttgtaatcactttaaacttttgttagttttc                  <  2:279092‑M2/141‑123 (MQ=255)                                                                                                                      aCCGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttgtaagttttc                  <  2:690046‑M2/141‑123 (MQ=255)                                                                                                                        cGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttgtaagttttcac                >  2:521739‑M2/1‑17 (MQ=255)                                                                                                                        cGAAGAATAGTATAGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttgtaagttttcac                <  1:485656‑M2/141‑125 (MQ=255)                                                                                                                                    taGCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttgtaagttttcacgtacacggtcaa    <  1:626020‑M2/141‑137 (MQ=255)                                                                                                                                      gCAactactacaataactgttaatactgtattaattgaacgtgtcattgtctgtctaattgatctattaacgatatcatcaatttgttctgttgtcgtaatcactttaaccttttgtaagttttcacttacacggtcaaac  <  1:600114‑M2/141‑139 (MQ=255)                                                                                                                                        |                                                                                                                                           TTTCAACTGACGTTTTTTCATTATTCCCCATAGCGGAACGGCAATGAAGATTGAAGAGAATACACCAGAAATCAATCCGATAAATAATGCTAAAGTAAAGTTGAATATCGTAGGAGCACCGAAGAATAGTATAGCAACTACTACTACAATAACTGTTAATACTGTATTAATTGAACGTGTCATTGTCTGTCTAATTGATCTATTAACGATATCATCAATTTGTTCTGTTGTCGTAATCACTTTAACCTTTTGTAAGTTTTCACGTACACGGTCA  >  USA300TCH1516_ALE/1747238‑1747511

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: ‑