Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,643,957	C→T	A38A (GCG→GCA)	cfiB_2 ←	2‑oxoglutarate carboxylase small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,643,957	0	C	T	100.0%	149.8 / NA	43	A38A (GCG→GCA)	cfiB_2	2‑oxoglutarate carboxylase small subunit
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/24);  total (19/24)

CCATAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACGGTT  >  USA300TCH1516_ALE/1643826‑1644092                                                                                                                                    |                                                                                                                                        ccATAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTa                                                                                                                                >  2:385434/1‑141 (MQ=255)    tAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATcc                                                                                                                             <  1:105288/141‑1 (MQ=255)    tAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATcc                                                                                                                             <  1:105214/141‑1 (MQ=255)    tAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATcc                                                                                                                             <  1:239757/141‑1 (MQ=255)              gAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAAt                                                                                                                   >  1:233984/1‑141 (MQ=255)                       cacaACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCaa                                                                                                          <  1:96877/141‑1 (MQ=255)                       cacaACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCaa                                                                                                          <  1:87622/141‑1 (MQ=255)                       cacaACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCaa                                                                                                          <  2:233719/141‑1 (MQ=255)                       cacaACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCaa                                                                                                          <  2:236757/141‑1 (MQ=255)                       cacaACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCaa                                                                                                          >  1:201612/1‑141 (MQ=255)                         caACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACa                                                                                                        >  1:5348/1‑141 (MQ=255)                          aaCCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAg                                                                                                       <  2:57106/141‑1 (MQ=255)                          aaCCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAg                                                                                                       <  1:327803/141‑1 (MQ=255)                          aaCCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAg                                                                                                       <  1:15144/141‑1 (MQ=255)                                    aGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGcc                                                                                             <  2:241027/141‑1 (MQ=255)                                           aTAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCa                                                                                      >  2:244913/1‑141 (MQ=255)                                                    aTGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAgcg                                                                             >  2:67068/1‑141 (MQ=255)                                                    aTGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAgcg                                                                             >  1:366810/1‑141 (MQ=255)                                                      gTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGcgcg                                                                           >  1:157832/1‑141 (MQ=255)                                                                        tGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGAt                                                         <  1:335955/141‑1 (MQ=255)                                                                            tCTTTAGACAAAGTGGGACCTACGCAATATACTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCa                                                     >  2:350496/1‑141 (MQ=255)                                                                                   aCAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGt                                              >  2:236648/1‑141 (MQ=255)                                                                                   aCAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGt                                              >  2:219470/1‑141 (MQ=255)                                                                                       aGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGc                                          >  2:222803/1‑141 (MQ=255)                                                                                          gggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAAt                                       <  2:91154/141‑1 (MQ=255)                                                                                           ggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAAtt                                      >  1:198835/1‑141 (MQ=255)                                                                                           ggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAAtt                                      >  2:62163/1‑141 (MQ=255)                                                                                           ggACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAAtt                                      >  1:234517/1‑141 (MQ=255)                                                                                                   gCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCtt                              <  1:9103/141‑1 (MQ=255)                                                                                                   gCAATATGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCtt                              <  1:84427/141‑1 (MQ=255)                                                                                                    cAATATACTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCttt                             <  1:350496/141‑1 (MQ=255)                                                                                                         tGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCat                        <  2:146498/141‑1 (MQ=255)                                                                                                         tGCTTCATCAGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCat                        <  1:317575/141‑1 (MQ=255)                                                                                                               atcaGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTc                  >  2:181071/1‑141 (MQ=255)                                                                                                               atcaGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTc                  >  1:390299/1‑141 (MQ=255)                                                                                                               atcaGCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTc                  >  1:201558/1‑141 (MQ=255)                                                                                                                   gCAATTTGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCt              <  1:222803/141‑1 (MQ=255)                                                                                                                        ttGAGTATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAAt         <  2:164319/141‑1 (MQ=255)                                                                                                                             tATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTTCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACgg    <  1:40544/141‑1 (MQ=255)                                                                                                                             tATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACgg    <  2:120837/141‑1 (MQ=255)                                                                                                                             tATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACgg    <  1:292656/141‑1 (MQ=255)                                                                                                                             tATGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACgg    <  1:68975/141‑1 (MQ=255)                                                                                                                               tGTAGTGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACGGtt  >  1:366466/1‑141 (MQ=255)                                                                                                                                    |                                                                                                                                        CCATAACCCGGATGAACGCCATCACAACCTGTAGAAGTTGCAATAGATAAGATGTTCGGAATATTTAAATATGAATCTTTAGACAAAGTGGGACCTACGCAATATGCTTCATCAGCAATTTGAGTATGTAGCGCATCTTTATCCCCTTCAGAATAGATTGCAACAGTTTGGATGCCTAAATCACGACAAGCGCGAATAATCCTAACTGCGATTTCACCGCGGTTTGCAATTAAAACCTTTTTCATTATTTCACCTTAAATAACGGTT  >  USA300TCH1516_ALE/1643826‑1644092

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑