Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,184,430	G→T	T172K (ACA→AAA)	rpsA_2 ←	30S ribosomal protein S1

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,184,430	0	G	T	100.0%	62.4 / NA	19	T172K (ACA→AAA)	rpsA_2	30S ribosomal protein S1
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (8/11);  total (8/11)

AAACTCTATGATTAGCAATGCGTTTAATTGGCTCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTGTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCATGTTTACGTGC  >  USA300TCH1516_ALE/2184293‑2184566                                                                                                                                          |                                                                                                                                         aacccctATGATTAGCAATGCGTTTAATTGGATCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCGTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTc                                                                                                                                       <  1:29768/136‑1 (MQ=255)                     cGTTTAATTGGCTCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGaa                                                                                                                   <  1:393927/141‑1 (MQ=255)                                    cTATATGCATAGTACATTTCAAAAATACCTTTTTCATCCTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAACTTTGTTCCGCaata                                                                                                    <  1:326207/141‑1 (MQ=255)                                            aTAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTtg                                                                                            <  1:485306/141‑1 (MQ=255)                                            aTAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTtg                                                                                            <  1:139985/141‑1 (MQ=255)                                                     ttCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCttt                                                                                   >  1:418445/1‑141 (MQ=255)                                                              aCCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTTTGCACCTTTGATAGCATc                                                                          <  1:497872/141‑1 (MQ=255)                                                               ccTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCt                                                                         >  1:62525/1‑141 (MQ=255)                                                                        tCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGGTGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCATTAATGTCTTGTGCACCTTTGATAGCCTCTTCAACCGAt                                                                >  1:184749/1‑141 (MQ=255)                                                                         cTTCAGCATTTTTCTATTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGAtt                                                               >  1:371232/1‑141 (MQ=255)                                                                           tCAGCATTTTTCTTTCTATATGCAGCTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGc                                                             <  1:134902/141‑1 (MQ=255)                                                                              gCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCAct                                                          <  1:265266/141‑1 (MQ=255)                                                                                 tttttCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCAattct                                                       >  1:106344/1‑141 (MQ=255)                                                                                                gTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCTACCGATTGCACTTCTTCATTtattagtggt                                        >  1:126076/1‑134 (MQ=255)                                                                                                   gTTAACACACCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATtgttgt                                     <  1:218092/141‑1 (MQ=255)                                                                                                         acacCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGGATGATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGTACTTCCTCATTTATAAATTGTTGTGCtttt                               >  1:62515/1‑141 (MQ=255)                                                                                                         acacCTTGATGATACATATCTTTTAAAATTTTTTTTCTATATTTAGAAGTAGCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCtttt                               >  1:390627/1‑141 (MQ=255)                                                                                                                           tCTTTTAAATTTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCa             <  1:212118/141‑1 (MQ=255)                                                                                                                           tCTTTTAAAATTTTTTTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCa             <  1:44460/141‑1 (MQ=255)                                                                                                                                      ttttttTCTATATTTAGGTTTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATTAGTTGTTGTGCTTTTTCTTCAATTGAGACTTCATGTTTACGTGc  >  1:104139/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                         AAACTCTATGATTAGCAATGCGTTTAATTGGCTCACTATATGCATAGTACATTTCAAAAATACCTTTTTCATCTTCAGCATTTTTCTTTTTAGATGTAGTTAACACACCTTGATGATACATATCTTTTAAAATTTTTGTTCTATATTTAGGATTATCTGAAATTTGTTCCGCAATAATATCTTGTGCACCTTTGATAGCATCTTCAACCGATTGCACTTCTTCATTTATAAATTGTTGTGCTTTTTCTTCAATTGAGACTTCATGTTTACGTGC  >  USA300TCH1516_ALE/2184293‑2184566

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: ‑