Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,775,913	C→T	G204D (GGT→GAT)	clpX ←	ATP‑dependent Clp protease ATP‑binding subunit ClpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,775,913	0	C	T	100.0%	71.2 / NA	21	G204D (GGT→GAT)	clpX	ATP‑dependent Clp protease ATP‑binding subunit ClpX
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (10/11);  total (10/11)

AAAGGCACCACCAAGAATAAATAAGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACACCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAA  >  USA300TCH1516_ALE/1775777‑1776057                                                                                                                                         |                                                                                                                                                 aaaGGCACCACCAAGAATAAATAAGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCCCCTGaaa                                                                                                                                      >  1:268401/1‑149 (MQ=255)       accaccAAGAATAAATAAGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCAc                                                                                                                                <  1:274371/149‑1 (MQ=255)           ccaAGAATAAATAAGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACgtgt                                                                                                                            <  2:149767/149‑1 (MQ=255)            caAGAATAAATAAGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGtt                                                                                                                           <  2:11379/149‑1 (MQ=255)                       aaGATATTGGTTGAAAAAATTAGAATCATTTCTTGAACTGTATGTTTGCGTCCACCTTGTGGCGGATCACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGtt                                                                                                                >  2:214700/1‑149 (MQ=255)                        aGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGttt                                                                                                               >  1:121360/1‑149 (MQ=255)                        aGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGttt                                                                                                               >  1:181996/1‑149 (MQ=255)                         gATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGtttt                                                                                                              >  1:198283/1‑149 (MQ=255)                                     aTCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTg                                                                                                  <  2:22968/149‑1 (MQ=255)                                            tGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAAtttt                                                                                           <  2:165460/149‑1 (MQ=255)                                             gAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTa                                                                                          <  1:231095/149‑1 (MQ=255)                                                     tCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTGTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTc                                                                                  >  2:237063/1‑149 (MQ=255)                                                      cTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCa                                                                                 <  2:252359/149‑1 (MQ=255)                                                       ttGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCAt                                                                                <  1:132277/149‑1 (MQ=255)                                                       ttGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCAt                                                                                <  1:214472/149‑1 (MQ=255)                                                                   tttGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACataaataa                                                                    >  2:33524/1‑149 (MQ=255)                                                                                     cGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTAt                                                  <  2:158165/149‑1 (MQ=255)                                                                                        aaCACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTATCaa                                               <  1:71930/149‑1 (MQ=255)                                                                                                                                   tgAACATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTc    >  2:72889/1‑149 (MQ=255)                                                                                                                                     aaCATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATCTTTTCaa  >  2:168814/1‑149 (MQ=255)                                                                                                                                     aaCATCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCaa  >  1:240094/1‑149 (MQ=255)                                                                                                                                         |                                                                                                                                                 AAAGGCACCACCAAGAATAAATAAGATATTTGTTGTATCAATTTGAATCATTTCTTGGTTTGGATGTTTGCGTCCACCTTGTGGCGGAACACTTGCAGTCGTACCTTCTAAGATTTTAAGCAATGCTTGTTGAACACCTTCACCTGAAACGTCACGTGTTATAGATGTGTTTTCAGATTTACGTGCAATTTTATCAATTTCATCTACATAAATAATACCTTTTTCGGCTTTATCAATGTCAAAGTCAGCTGCTTGAATTAATCTCAACAAGATATTTTCAA  >  USA300TCH1516_ALE/1775777‑1776057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑