Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	607,884	G→A	R209* (CGA→TGA)	dck ←	Deoxyadenosine/deoxycytidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	607,884	0	G	A	98.2%	171.7 / NA	55	R209* (CGA→TGA)	dck	Deoxyadenosine/deoxycytidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (34/20);  minor base C (0/1);  total (34/21)
Fisher's exact test for biased strand distribution p-value = 3.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTT  >  USA300TCH1516_ALE/607747‑608015                                                                                                                                          |                                                                                                                                    tataTGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTAATTGATTGTATTTTTGAATAATTCAAGc                                                                                                                                  <  2:198802/141‑1 (MQ=255)     tgtgAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAAtt                                                                                                                              <  2:591954/141‑1 (MQ=255)      gtgAATTAATGTATTCGATAGTATTGATAATATATTCGTTAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAGTAATTCAAGCAAttt                                                                                                                             <  1:684503/141‑1 (MQ=255)              aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTCCTTGTCGATATGTTTGTATAATTCAAGCATTTTTGTTTATc                                                                                                                     >  1:602753/1‑141 (MQ=255)              aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     >  2:531517/1‑141 (MQ=255)              aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     >  1:753119/1‑141 (MQ=255)              aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     <  1:765251/141‑1 (MQ=255)              aTGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATc                                                                                                                     >  2:11163/1‑141 (MQ=255)               tGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCa                                                                                                                    <  2:550705/141‑1 (MQ=255)                gTATTCGATAGAATTGATAAAATAATAGATAGTATTTGTCGATTATACAGAGAATATACACATATACGTTATGTCTGTGGCTTTCTATCGTGTATCGATCTACCTAAATGTTTGAATAATTCAAGCAAttttttttgacat                                                                                                                   >  2:286349/1‑136 (MQ=255)                      gATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAtt                                                                                                             >  1:771511/1‑141 (MQ=255)                       aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAttt                                                                                                            >  1:713761/1‑141 (MQ=255)                       aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAttt                                                                                                            <  1:820857/141‑1 (MQ=255)                       aTAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGAttt                                                                                                            >  1:5540/1‑141 (MQ=255)                             ttGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCACTTTTGTTTATCATAGGATTTAAAGAt                                                                                                      >  1:262489/1‑141 (MQ=255)                               gATAAAATACTCCATACTCTCAACGGAATATAAATTGAATATAAACAAATACGCTACGTCTTTATTCTTTTATCGTGTATCTACTGGTCGATATGTTTGAATAATTCAAGCATTTTTGTTTATCATAGGATTTAAAGATTc                                                                                                    >  2:407772/1‑141 (MQ=255)                               gATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGATATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTc                                                                                                    >  1:315843/1‑141 (MQ=255)                                  aaaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCggg                                                                                                 <  2:51045/141‑1 (MQ=255)                                   aaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGCAAATTTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCgggg                                                                                                >  1:170112/1‑141 (MQ=255)                                   aaaTAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCgggg                                                                                                >  1:720282/1‑141 (MQ=255)                                   aaaTAATCGATAATAACTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCgggg                                                                                                >  1:679551/1‑141 (MQ=255)                                        atCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCtt                                                                                           <  2:111484/141‑1 (MQ=255)                                          cGATAATATCTATGGAATATACATTGAATATAAACATATACGCCATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTAt                                                                                         <  1:342431/141‑1 (MQ=255)                                                tatCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGatat                                                                                   <  2:715485/141‑1 (MQ=255)                                                  tCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCa                                                                                 >  1:764871/1‑141 (MQ=255)                                                            ataCATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTaa                                                                       >  2:387503/1‑141 (MQ=255)                                                               cATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAatat                                                                    >  1:11597/1‑141 (MQ=255)                                                                      tataAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACg                                                             <  2:168690/141‑1 (MQ=255)                                                                       ataAACATATACGGTATGTCTTTAGTGTTTTATCGTGTATCTACTTGTCGATCTGTTTGAATAATTCAAGCAATTTTGTTTATTATAGGATTTAAAGATTGAGGGTCCTTATGGATATCATCTTCATTAATATTGATCCGt                                                            >  2:207651/1‑141 (MQ=255)                                                                         aaaCATATACTCTAGGTGTTTAGGCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCATTATGGATATCACATTCATTAATATTGATACGTAc                                                          <  1:182113/141‑1 (MQ=255)                                                                              aataCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTg                                                     <  2:907429/140‑1 (MQ=255)                                                                               ttaCGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTgg                                                    <  2:304147/140‑1 (MQ=255)                                                                               atactgtATTTCTTGAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCCAGCAATTTTGTTTATCATAGGATTTAACGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTgg                                                    <  2:751826/135‑1 (MQ=255)                                                                                     tATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTACTATTGATACGTACAACTGGACATGc                                              >  1:290334/1‑141 (MQ=255)                                                                                           tttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAACTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTCATATTGATACGTACAACTGGACATGCATTaaa                                        >  1:618197/1‑141 (MQ=255)                                                                                            ttAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAg                                       >  1:748719/1‑141 (MQ=255)                                                                                                 cTTTTATCGTGTATCTACTTGTCGGTGTGGTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTAtt                                  >  1:482022/1‑141 (MQ=255)                                                                                                 cTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTAtt                                  >  1:579338/1‑141 (MQ=255)                                                                                                      aTCGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGAGACCTTATGGATATCATATTCATTAATATTGATACGTCCAACTGGACATGCATTAAAGCTATTAATcc                             >  1:174731/1‑141 (MQ=255)                                                                                                        cGTGTATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCaa                           <  2:450228/141‑1 (MQ=255)                                                                                                         gtgtATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAAt                          >  2:39448/1‑141 (MQ=255)                                                                                                           gtATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCg                        >  1:725512/1‑141 (MQ=255)                                                                                                            tATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATCTTGATACGGACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                       <  1:633227/141‑1 (MQ=255)                                                                                                            tATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                       <  2:923177/141‑1 (MQ=255)                                                                                                            tATCTACTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGt                       <  2:155543/141‑1 (MQ=255)                                                                                                                  cTTGTCGATATGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGc                 <  1:530239/141‑1 (MQ=255)                                                                                                                  attGTCGATATGTTTGAATAATTCAAGCAATTTTGATTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATCTCATATTCATTAATATTGATACCTACAGCAGGACATGAATTAAACGAATTAATCCCATCGACATaac                 >  2:801331/2‑139 (MQ=255)                                                                                                                         atatGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTaaa          >  2:915236/1‑141 (MQ=255)                                                                                                                         atatGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTaaa          >  1:710743/1‑141 (MQ=255)                                                                                                                          tatGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAAt         >  1:643018/1‑141 (MQ=255)                                                                                                                           atGTTTGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATa        <  1:85777/141‑1 (MQ=255)                                                                                                                              tttGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTCTTAATCCAATCGTCATAGCGATTAAATAGCt     >  2:627171/1‑141 (MQ=255)                                                                                                                              tttGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCt     >  1:890916/1‑141 (MQ=255)                                                                                                                              tttGAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAACCGTCACAGCGTTTaaaacgct     >  2:802971/1‑136 (MQ=255)                                                                                                                                 gAATAATTCAAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGACATAGCGTTTAAATAGCtttt  >  2:143157/1‑141 (MQ=255)                                                                                                                                          |                                                                                                                                    TATATGTGAATTAATGTATTCGATAGAATTGATAAAATAATCGATAATATCTATGGAATATACATTGAATATAAACATATACGCTATGTCTTTAGTCTTTTATCGTGTATCTACTTGTCGATATGTTTGAATAATTCGAGCAATTTTGTTTATCATAGGATTTAAAGATTCGGGGTCCTTATGGATATCATATTCATTAATATTGATACGTACAACTGGACATGCATTAAAGCTATTAATCCAATCGTCATAGCGTTTAAATAGCTTTT  >  USA300TCH1516_ALE/607747‑608015

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: ‑