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%	99.4 / NA	31	A92V (GCA→GTA)	rpsI	30S ribosomal protein S9
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (19/12);  total (19/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAA  >  USA300TCH1516_ALE/2352678‑2352949                                                                                                                                          |                                                                                                                                       tatCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTAGTCAGGATCTACtt                                                                                                                                     >  1:55534/1‑141 (MQ=255)  atCGTCCGACAATTAATGTTTTGAGAATTGAGGTGAACGACGAGCTGCTCTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTc                                                                                                                                    <  1:684842/141‑1 (MQ=255)      tCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaat                                                                                                                                >  1:8751/1‑141 (MQ=255)      tCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaat                                                                                                                                >  1:8520/1‑141 (MQ=255)        ccaaaaTTAACGTTTTGAGAACTGAGGTTAACGACGAGCTGCTTTAAGGCCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCtaataa                                                                                                                              <  1:326042/137‑1 (MQ=39)            aaTTAACGTTTTGAGAATTGAGGCGAACGACCAGCTCCTTTAAGACCTCGTTTGTTACGTTCTTTCATACGTGGGTCACGAGTAAGCAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCa                                                                                                                          <  1:62542/141‑1 (MQ=38)                aaCGTTTTGATAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAg                                                                                                                      <  1:73143/141‑1 (MQ=255)                 aCGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTGATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGc                                                                                                                     >  1:167583/1‑141 (MQ=255)                             ttGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGGTCTACTTCTAATAATGCACGAGCGATTCCGTGACg                                                                                                         >  1:181341/1‑141 (MQ=255)                                 ggTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATa                                                                                                     >  1:413367/1‑141 (MQ=255)                                             gctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGCTTCCGTGCCGGATAGCTTGGGCTTGt                                                                                         >  1:26713/1‑141 (MQ=255)                                              ctgctTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGCTAGCTTGAGCTTGTc                                                                                        >  1:423044/1‑141 (MQ=255)                                                  tctAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGt                                                                                    <  1:310200/139‑1 (MQ=255)                                                      agcccTGGGTTTTTACGGTCCTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATCATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGaaa                                                                                <  1:205271/138‑1 (MQ=255)                                                           tGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGTGAGATTCCTTTACGGATAGCTTGAGCTTGTCCAGTGAAaccacc                                                                           <  1:366383/141‑1 (MQ=255)                                                           tGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCCGTGAAaccacc                                                                           >  1:729177/1‑141 (MQ=255)                                                           tGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTAAGCTAGTCCAGTGAAaccacc                                                                           >  1:428793/1‑141 (MQ=255)                                                                 tttACGTTCTTTCACACGTAGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATg                                                                     >  1:419748/1‑141 (MQ=255)                                                                    aCGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAAc                                                                  <  1:261426/141‑1 (MQ=255)                                                                           ttCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACt                                                           >  1:368309/1‑141 (MQ=255)                                                                           ttCATACGTGGGTCAAGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCCCCACCATGAACGTTAACt                                                           >  1:567814/1‑141 (MQ=255)                                                                                   tGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAAcatc                                                   >  1:706319/1‑141 (MQ=255)                                                                                       tCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAg                                               >  1:84996/1‑141 (MQ=255)                                                                                         aCGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGtt                                             <  1:421163/141‑1 (MQ=255)                                                                                             gtaagtaaTCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCt                                         <  1:396613/141‑1 (MQ=255)                                                                                                      ccAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCa                                >  1:444498/1‑141 (MQ=255)                                                                                                        aGCGCGTTTTAAAGAACCTCTGTATTCACGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCTCCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGt                              <  1:432082/141‑1 (MQ=255)                                                                                                             gTTTTAAAGAACCTCTGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACAt                         >  1:304169/1‑141 (MQ=255)                                                                                                                            tGTATTCAGGATCTACTTCTAATACTGCCAGAGCAATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGATTa          >  1:181774/1‑141 (MQ=255)                                                                                                                            tGTATTCAGGATCTACTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTa          >  1:691973/1‑141 (MQ=255)                                                                                                                                    ggATCTACTTCTAATAACGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTaaa  <  1:20670/141‑1 (MQ=255)                                                                                                                                          |                                                                                                                                       TATCGTCCGACAATTAACGTTTTGAGAATTGAGGTGAACGACGAGCTGCTTTAAGACCTGGTTTTTTACGTTCTTTCATACGTGGGTCACGAGTAAGTAATCCAGCGCGTTTTAAAGAACCTCTGTATTCAGGATCTGCTTCTAATAATGCACGAGCGATTCCGTGACGGATAGCTTGAGCTTGTCCAGTGAAACCACCACCATGAACGTTAACTAAAACATCATAGTTACCTTTAGTTTCAGTTACATCAAATGGTTGGTTTAAGTCTAAA  >  USA300TCH1516_ALE/2352678‑2352949

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑