Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,352,815	G→A	100%	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%	74.8 / NA	26	A92V (GCA→GTA)	rpsI	30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (16/10);  total (16/10)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGG  >  USA300TCH1516_ALE/2352685‑2352937                                                                                                                                   |                                                                                                                           cGACAATTAACGTTTTTAGAATTGAGGTGAACGACGATTTGCTTTAAGACCTTGTTTTTTACGTTCTTTCATACGTTGGTCACGAGTAAGTAATCCATCGCGTTTTAAAGAACCTCTTTATTCTTGATCTACTTCtaataa                                                                                                                  <  2:113133/141‑1 (MQ=37)       ttAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGCAACACACAAAGAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGAACTACTTCTAATAATGCACg                                                                                                            >  1:388932/1‑141 (MQ=37)        tAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGCTCTACTTCTAATAATGCACGa                                                                                                           >  1:193814/1‑141 (MQ=255)                      ttGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGGGCGGTAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                                                             >  1:287326/1‑141 (MQ=255)                                    gaGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATagcttgagctt                                                                               <  1:57658/141‑1 (MQ=255)                                      gctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGt                                                                             <  1:253302/141‑1 (MQ=255)                                       ctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTc                                                                            >  1:261481/1‑141 (MQ=255)                                                     ggTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCCGTGAAaccccca                                                              >  2:261216/1‑141 (MQ=255)                                                     ggTTTTTTACGTTCGTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccacca                                                              >  2:205760/1‑141 (MQ=255)                                                       gtttttCCGTGCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAaccaccacc                                                            <  2:57195/140‑1 (MQ=255)                                                        tttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTGCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCTAGTGAGAccaccacca                                                           >  2:887/1‑141 (MQ=255)                                                         ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACGCCCAt                                                          >  2:64001/1‑141 (MQ=255)                                                         ttttACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCAt                                                          <  2:309209/141‑1 (MQ=255)                                                         ttttACGTGCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCCCGCGCGCTCCCTTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCAt                                                          <  2:361051/141‑1 (MQ=255)                                                                   tttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAc                                                <  2:214237/141‑1 (MQ=255)                                                                      cATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTaa                                             >  1:317074/1‑141 (MQ=255)                                                                                   cGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTAGTCCAGTGGAACCACCAGCATGAACGATACCTGAAACATCCTCGttc                                >  2:136977/1‑140 (MQ=255)                                                                                       aaagtaaTCGAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCtt                            <  2:59366/140‑1 (MQ=255)                                                                                                    gcgTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTAc               >  1:323233/1‑141 (MQ=255)                                                                                                         ttAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAAAGTTAACTAAAACATCATAGTTCCCTTTGGGTTCCGTTGCATCaa          >  2:357721/1‑141 (MQ=255)                                                                                                          tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaaa         >  1:56542/1‑141 (MQ=255)                                                                                                          tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaaa         <  2:8159/141‑1 (MQ=255)                                                                                                          tAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAAATAAAACATCATAGTTACCTTTAGTTTCAGTTACATCaat         >  1:328434/1‑140 (MQ=255)                                                                                                                aCCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggttg   >  1:161239/1‑141 (MQ=255)                                                                                                                 ccTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAttggttgg  >  2:150898/1‑141 (MQ=255)                                                                                                                 ccTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAAtggttgg  <  2:287326/141‑1 (MQ=255)                                                                                                                                   |                                                                                                                           CGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGG  >  USA300TCH1516_ALE/2352685‑2352937

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: ‑