Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,372,751	A→T	L342* (TTA→TAA)	pbuG ←	Guanine/hypoxanthine permease PbuG

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,372,751	0	A	T	100.0%	75.3 / NA	29	L342* (TTA→TAA)	pbuG	Guanine/hypoxanthine permease PbuG
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (18/11);  total (18/11)

CACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCT  >  USA300TCH1516_ALE/2372621‑2372885                                                                                                                                   |                                                                                                                                       cACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTCACGGACTAAAGAACAGCGCATATAGGAaac                                                                                                                               >  2:72951/1‑140 (MQ=255)   cTGCAACTTCGAAACTTTTCCAGTTTTTCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACACCGATTAACGGACTAAAGACCCGCGCTTATAGGAaacaa                                                                                                                             >  2:110048/1‑140 (MQ=255)   cTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACCGCGCTTATAGCAaacac                                                                                                                             >  2:9827/1‑139 (MQ=255)               aaCTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACg                                                                                                                 >  2:180443/1‑140 (MQ=255)                   tttCCAGTTTATCTCAGCAAAGTTTGCAGCAATTAATACACCTAACACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAACGCTTATAACAAACAAAAACCTGTTaacacac                                                                                                             >  2:260249/1‑134 (MQ=255)                       cAGTTTATCTCAGCAAGGTTTGCAGCCATTAATACACCTACCACCACTAGGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGc                                                                                                         <  2:142980/140‑1 (MQ=255)                       cAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAATGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGc                                                                                                         <  2:212583/140‑1 (MQ=255)                             aTCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATcc                                                                                                   >  1:4869/1‑140 (MQ=255)                                tcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTTTTACAACAGTGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGt                                                                                                <  1:230628/140‑1 (MQ=255)                                tcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGt                                                                                                >  1:132585/1‑140 (MQ=255)                                tcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGt                                                                                                <  1:27220/140‑1 (MQ=255)                                      aaGTCTGCATCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATATGAAACAACATCCTGTTACGATACTAGCAAATCCTGTTCTAGc                                                                                          <  2:90766/140‑1 (MQ=255)                                              aGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAg                                                                                  <  1:145540/140‑1 (MQ=255)                                                 cATTAATACACCTACTACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCCACTTACAGTCTATATAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCaa                                                                               <  2:230859/140‑1 (MQ=255)                                                  aTTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAac                                                                              <  1:94143/140‑1 (MQ=255)                                                          acCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAg                                                                      <  1:180443/140‑1 (MQ=255)                                                                 accacTAAGGCTGGTGTCGTAACTGCACTTGTTCCAACAACGATTAACGCACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCCTCTACAGCAACACCTGAAGTTGATTc                                                               >  1:51672/1‑140 (MQ=255)                                                                                gtCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTCGATTCGATATAAGACattgt                                                >  2:139422/1‑140 (MQ=255)                                                                                gtCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAAACAACTGTTACGATAATAGCAAAACCTACTCAAACACCTACAGCAACACCTGAAATTGAGTCGCAAAaagaaagagt                                                >  2:132420/1‑135 (MQ=255)                                                                                  cGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACAGCGGAAGTTGATTCGCCCTCAGAAGttgttg                                              <  2:110063/140‑1 (MQ=255)                                                                                  cGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCCATATAAGCAGttggtg                                              >  1:266725/1‑140 (MQ=255)                                                                                            cTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTAGTAGTTGTTcc                                    >  2:208517/1‑140 (MQ=255)                                                                                               gTTACAACAGCGATTAACGGACTAAAGAACAGCGCTTATAAGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGAAACTACAGCACCACCTGAAGTTGATTAGATATAAGAACTTGTTGTAGTTGTTcacaa                                 >  2:56811/1‑136 (MQ=255)                                                                                               gTTACAACAGCGAATAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACGAGCAAATCCTGTTCTAACACCTACAGCAACACCTAAAGTTGATTCGATATAATAAATAGTTGTAGTTGTTCaaaa                                 >  2:23029/1‑140 (MQ=255)                                                                                                   caacaGCGATTAACGGACTAAAGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACt                             >  2:249560/1‑140 (MQ=255)                                                                                                                       aaGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAATTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaa         >  1:171051/1‑140 (MQ=255)                                                                                                                        aGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaaa        <  1:226152/140‑1 (MQ=255)                                                                                                                        aGAACAGCGCTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaaa        >  1:158050/1‑140 (MQ=255)                                                                                                                              gcgcTTATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTCGATTCCATATAAGAAGTTGTCGTAGTTATTCAAAAAACTGCTCCCACAAACATCGCTAAAGAATCt  >  2:55260/1‑140 (MQ=255)                                                                                                                                   |                                                                                                                                       CACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCT  >  USA300TCH1516_ALE/2372621‑2372885

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: ‑