Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	596,093	T→G	6.9%	A375A (GCT→GCG)	fusA →	Elongation factor G

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	596,093	0	T	G	6.9%	177.5 / 4.4	56	A375A (GCT→GCG)	fusA	Elongation factor G
Reads supporting (aligned to +/- strand):  ref base T (25/27);  new base G (2/2);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

TATTCAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTGACCAAG  >  USA300TCH1516_ALE/595959‑596229                                                                                                                                       |                                                                                                                                         tATTCAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCg                                                                                                                                    >  1:782922/1‑141 (MQ=255) tATTCAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCGGCTGCg                                                                                                                                    >  2:16872/1‑141 (MQ=255)     cAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAg                                                                                                                                >  1:464372/1‑141 (MQ=255)     cAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAg                                                                                                                                >  1:596164/1‑141 (MQ=255)       ggTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGt                                                                                                                              <  2:217347/141‑1 (MQ=255)          aCAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCtt                                                                                                                           >  1:198911/1‑141 (MQ=255)                aCATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGAt                                                                                                                     >  2:112427/1‑141 (MQ=255)                 cATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGGAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATa                                                                                                                    >  2:283173/1‑141 (MQ=255)                   tCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACa                                                                                                                  >  2:38802/1‑141 (MQ=255)                   ccTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACa                                                                                                                  <  1:574396/140‑1 (MQ=255)                         tCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACt                                                                                                            <  2:333206/141‑1 (MQ=255)                           aTACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTCGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTgg                                                                                                          <  1:582827/141‑1 (MQ=255)                           aTACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTgg                                                                                                          <  2:93465/141‑1 (MQ=255)                            tACGTTAAGAGCTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGt                                                                                                         <  1:615895/141‑1 (MQ=255)                            tACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGt                                                                                                         >  2:51335/1‑141 (MQ=255)                                 tAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATAc                                                                                                    <  1:420866/141‑1 (MQ=255)                                     aaCTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTa                                                                                                >  1:274410/1‑141 (MQ=255)                                     aaCTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTa                                                                                                >  1:379056/1‑141 (MQ=255)                                         ctactaAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTAtgtg                                                                                            >  1:212050/1‑141 (MQ=255)                                         ctactaAAGCTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTAtgtg                                                                                            >  1:692483/1‑141 (MQ=255)                                          tactaAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATgtgg                                                                                           <  1:597920/141‑1 (MQ=255)                                                     aacgtgaacgtgTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATg                                                                                <  1:2750/141‑1 (MQ=255)                                                       cgtgaacgtgTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGAc                                                                              <  1:255410/141‑1 (MQ=255)                                                        gtgaacgtgTAGGTCGTTTATTACAAATTCACGCTAACTCTCGGCAAGAAAGCGATACTGTAGACTCGGTAGATATGGCGGCGGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACa                                                                             >  1:116091/1‑141 (MQ=255)                                                           aacgtgTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTa                                                                          >  2:215385/1‑141 (MQ=255)                                                            acgtgTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTAt                                                                         >  2:261368/1‑141 (MQ=255)                                                             cgtgTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATc                                                                        >  1:352508/1‑141 (MQ=255)                                                                     tCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATc                                                                <  2:312016/141‑1 (MQ=255)                                                                       gTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCaa                                                              <  1:274898/141‑1 (MQ=255)                                                                         ttattaCGAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAGATGACATTATCTTGGAATCAATg                                                            >  1:624725/1‑141 (MQ=255)                                                                           attaCAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGa                                                          <  1:316684/141‑1 (MQ=255)                                                                           attaCAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGa                                                          <  2:112324/141‑1 (MQ=255)                                                                             taCAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAAt                                                        <  1:602804/141‑1 (MQ=255)                                                                                 aaTGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTccc                                                    >  1:39273/1‑141 (MQ=255)                                                                                      aCGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGc                                               <  1:100261/141‑1 (MQ=255)                                                                                       cGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGcc                                              >  1:111703/1‑141 (MQ=255)                                                                                        gCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCGGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCa                                             <  1:109047/141‑1 (MQ=255)                                                                                        gCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCGGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCa                                             <  1:503768/141‑1 (MQ=255)                                                                                           aaCTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGtt                                          <  1:233147/141‑1 (MQ=255)                                                                                            aCTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGAAATCAATGGAATTCCCAGAGCCAGTTa                                         >  1:611208/1‑141 (MQ=255)                                                                                             cTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTAt                                        >  2:254988/1‑141 (MQ=255)                                                                                               cACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTc                                      >  1:657202/1‑141 (MQ=255)                                                                                               cACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTc                                      >  1:286648/1‑141 (MQ=255)                                                                                                 cGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCAc                                    <  2:233329/141‑1 (MQ=255)                                                                                                   tCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACtt                                  <  1:293116/141‑1 (MQ=255)                                                                                                               tACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCCTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGcc                      <  1:183183/141‑1 (MQ=255)                                                                                                                 cTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCaa                    >  2:169621/1‑141 (MQ=255)                                                                                                                     aatccctGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATc                <  1:703042/136‑1 (MQ=255)                                                                                                                      taCTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCt               >  1:5850/1‑141 (MQ=255)                                                                                                                           tGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGc          <  1:92490/141‑1 (MQ=255)                                                                                                                           tGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGc          <  1:231197/141‑1 (MQ=255)                                                                                                                           gggAGATATCGCTGCCGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGc          <  1:149424/140‑1 (MQ=255)                                                                                                                             gagaTATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTg        <  2:246655/141‑1 (MQ=255)                                                                                                                             gagaTATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTg        >  1:376976/1‑141 (MQ=255)                                                                                                                              agaTATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTGa       <  2:307778/141‑1 (MQ=255)                                                                                                                                   tCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTGACCAAg  <  1:622302/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                         TATTCAGGTACAATGACATCTGGTTCATACGTTAAGAACTCTACTAAAGGTAAACGTGAACGTGTAGGTCGTTTATTACAAATGCACGCTAACTCACGTCAAGAAATCGATACTGTATACTCTGGAGATATCGCTGCTGCGGTAGGTCTTAAAGATACAGGTACTGGTGATACTTTATGTGGTGAGAAAAATGACATTATCTTGGAATCAATGGAATTCCCAGAGCCAGTTATTCACTTATCAGTAGAGCCAAAATCTAAAGCTGACCAAG  >  USA300TCH1516_ALE/595959‑596229

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