Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,775,556	G→A	P323L (CCT→CTT)	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	1,775,556	0	G	A	100.0%	99.7 / NA	31	P323L (CCT→CTT)	clpX	ATP‑dependent Clp protease ATP‑binding subunit ClpX
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/13);  total (18/13)

CTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTTCGT  >  USA300TCH1516_ALE/1775413‑1775697                                                                                                                                                |                                                                                                                                              ctATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATTTTGTTTCACAAGTGCATTTTTAAGTTg                                                                                                                                           >  2:259337/1‑148 (MQ=255)      aTTGAACGTAAACCACGCGCACCTGTTTTTTTTTTTTTTTCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTTCGttt                                                                                                                                      >  2:204914/1‑147 (MQ=255)      aTTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTa                                                                                                                                      >  2:301818/1‑148 (MQ=255)            cGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGt                                                                                                                                >  2:56435/1‑148 (MQ=255)               aaaCCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGtttt                                                                                                                             <  1:50226/148‑1 (MQ=255)               aaaCCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGtttt                                                                                                                             <  1:41468/148‑1 (MQ=255)                            cTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTAc                                                                                                                <  1:274496/148‑1 (MQ=255)                                        cAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTc                                                                                                    >  1:211948/1‑148 (MQ=255)                                        cAATTGCTTTTTCACTAATAGCTGATAAAGCTTCTTCAGTGTACTCTAACTCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTc                                                                                                    >  2:219179/1‑148 (MQ=255)                                              cTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAAtt                                                                                              <  2:174073/148‑1 (MQ=255)                                                          ttGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTgg                                                                                  <  2:359702/148‑1 (MQ=255)                                                              tGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGcaca                                                                              >  1:328549/1‑148 (MQ=255)                                                                 gaaaGCTTCGTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGGATATGGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGt                                                                           >  1:78828/2‑148 (MQ=255)                                                                            cAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTc                                                                >  2:291380/1‑148 (MQ=255)                                                                                                  ttcTAATTCCAGCTATCGAGTATATTGTGTCACAAGTGCATTTTTAAGATGCGTTAAGATGTTTTTCAACGCAGCTACAGCTAATGTTTCTAAATTAGCTACAATTGGCACACGGCCGATAAATTCAGGAATCAAACCATAGGCCTGc                                          <  2:284419/147‑1 (MQ=255)                                                                                                      aaTTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAAt                                      >  1:99387/1‑148 (MQ=255)                                                                                                      aaTTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAAt                                      >  1:120095/1‑148 (MQ=255)                                                                                                                ttttAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCg                            >  1:223497/1‑148 (MQ=255)                                                                                                                          ttGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCt                  <  2:210443/148‑1 (MQ=255)                                                                                                                          ttGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCt                  >  1:282523/1‑148 (MQ=255)                                                                                                                          ttGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCt                  <  2:244517/148‑1 (MQ=255)                                                                                                                          ttGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCt                  <  2:268215/148‑1 (MQ=255)                                                                                                                               tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCtaataa             >  2:343405/1‑148 (MQ=255)                                                                                                                               tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCtaataa             >  1:267844/1‑148 (MQ=255)                                                                                                                               tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCtaataa             >  2:346594/1‑148 (MQ=255)                                                                                                                               tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCtaataa             >  1:371280/1‑148 (MQ=255)                                                                                                                               tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCtaataa             >  1:53521/1‑148 (MQ=255)                                                                                                                                          tttttAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTTCGt  <  1:177658/148‑1 (MQ=255)                                                                                                                                          tttttAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTTCGt  <  2:230379/148‑1 (MQ=255)                                                                                                                                          tttttAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTTCGt  <  2:188922/148‑1 (MQ=255)                                                                                                                                          tttttAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTTCGt  <  2:147599/148‑1 (MQ=255)                                                                                                                                                |                                                                                                                                              CTATGATTGAACGTAAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTTCGT  >  USA300TCH1516_ALE/1775413‑1775697

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑