Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	818,312	T→A	10.9%	N97K (AAT→AAA)	USA300HOU_RS04005 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	818,312	0	T	A	10.9%	105.9 / 5.2	44	N97K (AAT→AAA)	USA300HOU_RS04005	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (25/14);  new base A (2/3);  total (27/17)
Fisher's exact test for biased strand distribution p-value = 3.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.42e-01

AATATACATTTGAAAGAAATTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGAAGACATT  >  USA300TCH1516_ALE/818172‑818450                                                                                                                                             |                                                                                                                                           aataTACATTTGAAAGAAATTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAAt                                                                                                                                            <  2:80235/141‑1 (MQ=255)    ataCATTTGAAAGAAATTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTg                                                                                                                                         <  1:332601/141‑1 (MQ=255)     taCATTTGAAAGAAATTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGc                                                                                                                                        <  2:71520/141‑1 (MQ=255)             aaagaaaTTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTgatgat                                                                                                                                >  2:33269/1‑141 (MQ=255)                  aaTTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAAt                                                                                                                           >  2:7398/1‑141 (MQ=255)                   aTTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATAAAAta                                                                                                                          >  1:228101/1‑140 (MQ=255)                      gATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGaaa                                                                                                                       >  1:297591/1‑141 (MQ=255)                       atcatcTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCCTACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGACTGATGACACAATGaaaa                                                                                                                      >  1:113139/1‑140 (MQ=255)                        tcatcTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAACAAATTTGCCTACTGATAAAATAAACGt                                                                                                                     >  2:17000/1‑141 (MQ=255)                              gaGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTGAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGaa                                                                                                               <  1:342365/140‑1 (MQ=255)                                   aaaCTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTaa                                                                                                          >  2:8765/1‑141 (MQ=255)                                                    aaaaaTAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACg                                                                                         <  1:7398/141‑1 (MQ=255)                                                       aaTAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCtt                                                                                      <  1:34753/141‑1 (MQ=255)                                                        aTAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTg                                                                                     <  2:178417/141‑1 (MQ=255)                                                        aTAGTAAAGAATTTAAAGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTg                                                                                     <  2:290848/141‑1 (MQ=255)                                                        aTAGTAAAGAAGTTAAGGAACTACAAGAAGATGTTAAAAACCATCTCAGACCTAAATTTGAAGCATAATATAATGCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTg                                                                                     <  1:130522/141‑1 (MQ=255)                                                             aaaGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAAATTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAAt                                                                                >  2:27996/1‑141 (MQ=255)                                                             aaaGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAAATTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAAt                                                                                >  2:27961/1‑141 (MQ=255)                                                               aGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATga                                                                              >  2:285169/1‑141 (MQ=255)                                                               aGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATga                                                                              >  1:99336/1‑141 (MQ=255)                                                                     tAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAgaagaa                                                                        >  1:64519/1‑141 (MQ=255)                                                                       aGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAgg                                                                      >  1:106247/1‑141 (MQ=255)                                                                            cTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGAAGCg                                                                 >  2:334511/1‑141 (MQ=255)                                                                                  gaagaTGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACCCTTACAACTGAGAAAAAGAATGAGatataa                                                           >  2:101828/1‑140 (MQ=255)                                                                                       tGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGCAGGATGGGATATATTAAtt                                                      >  2:290568/1‑141 (MQ=255)                                                                                        gTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTa                                                     >  1:227161/1‑141 (MQ=255)                                                                                                  aTCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCa                                           <  1:315871/141‑1 (MQ=255)                                                                                                  aTCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAAATTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCa                                           <  1:27961/141‑1 (MQ=255)                                                                                                  aTCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAAATTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCa                                           <  1:27996/141‑1 (MQ=255)                                                                                                   tctcATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCAt                                          <  2:160366/141‑1 (MQ=255)                                                                                                          ccaaaaaTTGAAGCATATTATAAGTCAGCAAAAAAATTGCCTGATGATACAATGAAAGTTAAGAAAATAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTa                                   <  2:298278/138‑1 (MQ=255)                                                                                                                  tGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCAAGCCAGGAACGAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATCTaatca                           >  1:65474/1‑141 (MQ=255)                                                                                                                  tGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATAAGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTaatca                           >  2:3484/1‑141 (MQ=255)                                                                                                                  tGAAGCATATTATAAGTAAGCACAAGATTTTCCGGTTTAGACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTaatca                           >  1:149038/1‑141 (MQ=255)                                                                                                                    aaGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTaatcaat                         >  1:176609/1‑141 (MQ=255)                                                                                                                    aaGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTaatcaat                         >  2:55758/1‑141 (MQ=255)                                                                                                                     aGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTaatcaatc                        >  1:162646/1‑141 (MQ=255)                                                                                                                     aGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATACATAGGAGTATGTaatcaatc                        >  2:280418/1‑141 (MQ=255)                                                                                                                            aaaaaGTCAGGAAAAAATTTGCCTGATGATAAAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAg                 <  2:335456/138‑1 (MQ=255)                                                                                                                               aaGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGtat              >  1:165620/1‑141 (MQ=255)                                                                                                                                    aGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGa         >  1:312297/1‑141 (MQ=255)                                                                                                                                     gCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGaa        <  1:263869/141‑1 (MQ=255)                                                                                                                                     gCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGaa        <  1:285169/141‑1 (MQ=255)                                                                                                                                         aaaaTTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGAGGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGAAGACa    >  1:188983/1‑141 (MQ=255)                                                                                                                                           aaTTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGAAGACAtt  <  2:149038/141‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           AATATACATTTGAAAGAAATTGATCATCTAAGTAAAACTGATACAACTGATAAAAATAGTAAAGAATTTAAGGCACTACAAGAAGATGTTAAAAACCATCTCATACCTAAATTTGAAGCATATTATAAGTCAGCAAAAAATTTGCCTGATGATACAATGAAAGTTAAGAAATTAAAAAAAGAATATATGACGCTTGCAAATGAGAAGAAGGATGCGATATATCAATTAAAAAAATTCATAGGTTTATGTAATCAATCTATCAAGTATAACGAAGACATT  >  USA300TCH1516_ALE/818172‑818450

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑