Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,605,275	G→T	82.6%	R199L (CGT→CTT)	USA300HOU_1490 →	integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,605,275	0	G	T	82.6%	49.7 / 9.1	29	R199L (CGT→CTT)	USA300HOU_1490	integrase
Reads supporting (aligned to +/- strand):  ref base G (2/3);  new base T (9/15);  total (11/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.81e-01

ATTTTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGAT  >  CP000730/1605141‑1605405                                                                                                                                       |                                                                                                                                   atattACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCTAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCGACAGATACTTGATCa                                                                                                                              <  1:246167/138‑1 (MQ=255) aTTTTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCa                                                                                                                              >  2:188065/1‑141 (MQ=255) aTTTTACAATGATCCAAATGAATAAATGTTAACCAACGGCAAAATGCCTAAAATAAGAAAAACAATAGACGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCa                                                                                                                              <  1:208858/141‑1 (MQ=255)       cAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACt                                                                                                                        <  1:17278/141‑1 (MQ=255)          ttATCCAAATGAATATTTGTTAACTAATTTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTaaa                                                                                                                     <  1:132960/141‑1 (MQ=255)              ccAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGat                                                                                                                 <  1:24160/141‑1 (MQ=255)                         tttGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGATaca                                                                                                      >  2:130862/1‑141 (MQ=255)                                             ttCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTaa                                                                                  >  1:280314/1‑141 (MQ=255)                                               ccTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAAtt                                                                                >  2:189076/1‑141 (MQ=255)                                                     agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAGTGATAATAAGTTACACAAGCGAAATCGCATTTTCATTGCCCGc                                                                          >  1:165546/1‑141 (MQ=255)                                                     agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGc                                                                          <  2:139698/141‑1 (MQ=255)                                                     agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGc                                                                          <  2:295578/141‑1 (MQ=255)                                                          aaaaaCAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGTTAAATCGCATTTCAATTGCCAGCATCtt                                                                     <  2:306720/141‑1 (MQ=255)                                                          aaaaaCAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCtt                                                                     >  1:137377/1‑141 (MQ=255)                                                                aaTAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGt                                                               <  2:41972/141‑1 (MQ=255)                                                                  aagagGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTAc                                                             <  2:57584/140‑1 (MQ=255)                                                                   atattttttCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCTAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACa                                                            <  2:81875/133‑1 (MQ=255)                                                                   agagGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTAAACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACa                                                            >  1:169801/1‑141 (MQ=255)                                                                     agGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTCGATCATATACTAAATGATAAGAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAgg                                                          <  2:170/141‑1 (MQ=255)                                                                      agATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGc                                                         <  2:48542/140‑1 (MQ=255)                                                                                               aTGTACAACTATTTAGAAATGAACCAAGTCCTACAAATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTACCAGCATCTTAGAAGTACAGGCTTTACCTGGTATGCCCATAGGAGaa                                >  2:37835/1‑141 (MQ=255)                                                                                                      aCTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACaaa                         >  1:83629/1‑140 (MQ=255)                                                                                                               aaaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACaaaaaaaaaaaa                <  2:329458/141‑11 (MQ=255)                                                                                                               aaaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAgg                >  1:328749/1‑141 (MQ=255)                                                                                                                   gAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGaaaa            <  2:207773/141‑1 (MQ=255)                                                                                                                       cAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGat        >  2:238707/1‑141 (MQ=255)                                                                                                                         aGTCCTACAGATACTTGAACATATACTAAATGAAAATAAGTTACACAAGCGAACTCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGTAAAAAGatat      <  2:141247/141‑1 (MQ=255)                                                                                                                            ccTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGa   <  1:277264/141‑1 (MQ=255)                                                                                                                             cTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGAt  <  2:280314/141‑1 (MQ=255)                                                                                                                                       |                                                                                                                                   ATTTTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGAT  >  CP000730/1605141‑1605405

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: ‑