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
A3 F75 I0 R1	16	35.0	795252	94.4%	750717	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,124	G→A	72.5%	P174L (CCG→CTG)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,124	0	G	A	72.5%	36.2 / 19.7	33	P174L (CCG→CTG)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (2/7); new base A (15/9); total (17/16)
Fisher's exact test for biased strand distribution p-value = 5.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.34e-01

GTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTC  >  USA300TCH1516_ALE/2027985‑2028248

gaaGATGTTAACCGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCgg                                                                                                                             <  1:106592/139‑1 (MQ=255)

gTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCgg                                                                                                                             <  1:9716/141‑1 (MQ=255)

  atatatTAACTTTATAGTTATCCGTTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCa                                                                                                                           <  2:305004/139‑1 (MQ=255)

         aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAc                                                                                                                    >  2:54360/1‑141 (MQ=255)

             gTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGc                                                                                                                >  1:134038/1‑141 (MQ=255)

               ataGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTACTTAACCAGCAATATAACCTGCAc                                                                                                              >  2:265508/1‑141 (MQ=255)

               ataGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCAc                                                                                                              >  1:30173/1‑141 (MQ=255)

                       ccGGTTTCATCATTTCTTTAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTa                                                                                                      <  2:271884/141‑1 (MQ=255)

                        cGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTaa                                                                                                     <  1:99768/141‑1 (MQ=255)

                        cGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTaa                                                                                                     >  1:124417/1‑141 (MQ=255)

                         ggTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTaaa                                                                                                    >  2:221444/1‑141 (MQ=255)

                         ggTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAACTGCACTTTACCTaaa                                                                                                    >  2:108263/1‑141 (MQ=255)

                           tttCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAAt                                                                                                  >  2:230781/1‑141 (MQ=255)

                            ttCATCATTTCTTCAATATGAATATTGTTATTGTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAAtg                                                                                                 >  1:208736/1‑141 (MQ=255)

                                     tcttcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTaaca                                                                                        <  1:239646/141‑1 (MQ=255)

                                      cttcAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTaacaa                                                                                       >  2:156082/1‑141 (MQ=255)

                                              tGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGta                                                                               <  1:336934/141‑1 (MQ=255)

                                                  tagtGTTATTGTCAACTTTATATGATTTTGCAGTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGtattat                                                                           <  1:153605/138‑1 (MQ=255)

                                                         aTTTTCAAATTAATATGATATTTCATTCACGTAAGTACTTCAATAAAAAGCAGCTACATGTAAATGAACATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCtt                                                                    <  1:59611/141‑1 (MQ=255)

                                                              ctaCTTTATATGATTTTTCATTCACGTAAGGACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCCGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAatat                                                               >  2:390789/3‑141 (MQ=255)

                                                                aCTTTATATGATTTTTCATACACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATAttt                                                             <  1:220672/141‑1 (MQ=255)

                                                                    tataTGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTACTATTAGAACTCACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAg                                                         <  1:290336/141‑1 (MQ=255)

                                                                       agcaTTTTTCCTTCACGTAAGTGTTTCCATCAACATCAGTTACATGTAAATTAATATTGTAATTACCCGGGAAGATAACCGGCACCTTGCCTCTATTGTTTCTACGAATTATGGTATTATTTTCCTTAATATTTGCAGCtt                                                      <  2:162606/138‑1 (MQ=255)

                                                                                          aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAg                                   >  1:180125/1‑141 (MQ=255)

                                                                                          aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAg                                   <  1:156082/141‑1 (MQ=255)

                                                                                          aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAAAATAGACATTAGGGTGAATGCCAGCGGCTATTATAGTATTATTTTCATTAATATTTGCAGCTTTTGTTAAGTCAAtatatat                                   >  2:386119/1‑140 (MQ=255)

                                                                                           gTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAgg                                  >  1:320880/1‑141 (MQ=255)

                                                                                               ttCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGc                              <  2:57757/141‑1 (MQ=255)

                                                                                                tCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTATAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGcc                             <  1:54360/141‑1 (MQ=255)

                                                                                                    tAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTTCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAAGATGTAGGTCGCCAAtt                         >  1:317730/1‑141 (MQ=255)

                                                                                                      aaaaGCAGCTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTcc                       <  1:230781/141‑1 (MQ=255)

                                                                                                       aaaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCa                      >  1:189697/1‑141 (MQ=255)

                                                                                                             gcTACATGTAAATTAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTCAGTCAATATGTAGGTCGCCAATTCCATGTTGa                >  2:259007/1‑141 (MQ=255)

                                                                                                                         ttAATATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCt    <  2:180125/141‑1 (MQ=255)

                                                                                                                           aaTATTGTAATTAACCAGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTc  <  2:188330/141‑1 (MQ=255)

GTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTC  >  USA300TCH1516_ALE/2027985‑2028248

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