Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,352,815	G→A	A92V (GCA→GTA)	rpsI ←	30S ribosomal protein S9

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,352,815	0	G	A	100.0%	77.3 / NA	26	A92V (GCA→GTA)	rpsI	30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/16);  total (10/16)

TCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGT  >  USA300TCH1516_ALE/2352683‑2352944                                                                                                                                     |                                                                                                                                  tCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATAAAGGGAGTGGGAAAGAACCTCTGTATTCAGGATCTACTTCtaat                                                                                                                           >  1:258948/1‑141 (MQ=37)       aaTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTCATCCGGCGCGTTTTAAAGAACCTCTGTATTAAGGATCTACTTCTAATAATGCa                                                                                                                     >  1:215409/1‑141 (MQ=255)        aTTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCAc                                                                                                                    >  1:459663/1‑141 (MQ=255)                 ttGAGAATTGAGGTGAACGACGCGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTAATACGTAGGTCACGAGTAAGTAATCCAGCGCGTTTGAAAGAAGCTCTGCATTCAGGATCTACTTCTAATAATGCACGAGCGATTc                                                                                                           <  1:346443/141‑1 (MQ=38)                     gaATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATAGAGGATGTACTTCTAATAATGCACGAGCGATTCCGTg                                                                                                       >  1:338585/1‑141 (MQ=255)                     gaATTGAGGTGAACGACGAGCTCACCTAATGCCTGGTTATTTCTGACCGGCGGTTCGGGTGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTg                                                                                                       <  1:361926/141‑1 (MQ=255)                        ttGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                                                                    >  1:356893/1‑141 (MQ=255)                            ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATa                                                                                                >  1:250269/1‑141 (MQ=255)                                         ctgctTTAAGACCTTGTTTTTTACGTTCCTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                                                                   <  1:212624/141‑1 (MQ=255)                                             tttAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGGGCTTGTCCAgg                                                                               >  1:181694/1‑140 (MQ=255)                                                     cTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATTAAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAacccc                                                                       >  1:344201/1‑139 (MQ=255)                                                         ttttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGGGCTTGTCCAGTGAAaccaccacc                                                                   >  1:234409/1‑141 (MQ=255)                                                           ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCAt                                                                 <  1:280514/141‑1 (MQ=255)                                                           ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAACGCTCTGCCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCCCCACCAt                                                                 >  1:14101/1‑141 (MQ=255)                                                             ttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGa                                                               <  1:220110/141‑1 (MQ=255)                                                             ttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGa                                                               <  1:355004/141‑1 (MQ=255)                                                                                ggTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGTACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatcat                                            <  1:347313/141‑1 (MQ=255)                                                                                      caggaagtaaTCCATCGCGTTTTAAAGAACCTTTGTATTCAGGATCTACTACTCCTAAAGCACTAGGGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTAc                                      <  1:237574/137‑1 (MQ=255)                                                                                        gtaaggaaTCCAGCGCGTTTTGAAGAACCTCTGTATTCAGGATCTACTTCGAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCt                                    <  1:182/141‑1 (MQ=255)                                                                                                         ttttAAAGAACCTCTGTATTCAGGATCTACTTCCAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCCCCCCAAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATc                   <  1:472442/141‑1 (MQ=255)                                                                                                            tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAACGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaaa                <  1:204832/141‑1 (MQ=255)                                                                                                               aGAACCTCTGTATTCAGGATCTACTTCTAATAATGCCAGTGAGGTTGCGGGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtgg             <  1:259422/141‑1 (MQ=255)                                                                                                                gAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggt            <  1:400959/141‑1 (MQ=255)                                                                                                                          tttCGGGATCTACTTCTAATAATGCACGGGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGt  <  1:40408/140‑1 (MQ=255)                                                                                                                          aTTCCGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGt  <  1:155168/141‑1 (MQ=255)                                                                                                                          aTTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGt  <  1:322344/141‑1 (MQ=255)                                                                                                                                     |                                                                                                                                  TCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGT  >  USA300TCH1516_ALE/2352683‑2352944

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: ‑