Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A19 F106 I0 R1	88	30.3	670850	93.2%	625232	140.9

Breseq alignment

BRESEQ :: Evidence

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: `‑`

GATK/CNVnator alignment

N/A