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
A1 F70 I1 R1	12	27.5	645536	94.4%	609385	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,191	C→A	A152S (GCA→TCA)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,191	0	C	A	96.8%	90.6 / NA	31	A152S (GCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (11/19); minor base T (1/0); total (12/19)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAT  >  USA300TCH1516_ALE/2028057‑2028328

tGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCttt                                                                                                                                     <  1:145109/141‑1 (MQ=255)

         attcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTc                                                                                                                            <  1:150879/141‑1 (MQ=255)

              cGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAatat                                                                                                                       <  1:86479/141‑1 (MQ=255)

                   gTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAgg                                                                                                                  <  1:197406/141‑1 (MQ=255)

                        tCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGTAACTGATGGTAAGTAAATATCTTGGTCGcc                                                                                                             >  1:248595/1‑141 (MQ=255)

                                  gcagcTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGt                                                                                                   >  1:272805/1‑141 (MQ=255)

                                     gcTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGa                                                                                                >  1:262995/1‑141 (MQ=255)

                                      cTACATGTAAATTAATATAGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATACGTAAGTCGCCAATTCCATGTTGaa                                                                                               <  2:76838/141‑1 (MQ=255)

                                           tGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGt                                                                                          <  1:7474/141‑1 (MQ=255)

                                                   aaTATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTc                                                                                  >  2:99806/1‑141 (MQ=255)

                                                   aaTATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTc                                                                                  <  1:103131/141‑1 (MQ=255)

                                                      atTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTccaa                                                                               >  1:25401/1‑139 (MQ=255)

                                                           aaTTAACCGGCAATATAACCTGCACGTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTtat                                                                          <  1:312085/141‑1 (MQ=255)

                                                              tAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTtatata                                                                       <  2:142611/141‑1 (MQ=255)

                                                                aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTGCGTGCAACGATATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                                     <  2:227921/141‑1 (MQ=255)

                                                                aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                                     >  1:192993/1‑141 (MQ=255)

                                                                aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                                     <  2:62445/141‑1 (MQ=255)

                                                                aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACa                                                                     <  2:119716/141‑1 (MQ=255)

                                                                                  aCTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGc                                                   <  1:269113/141‑1 (MQ=255)

                                                                                             aaTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCa                                        >  2:26733/1‑141 (MQ=255)

                                                                                               tgtgTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACt                                      <  1:211654/141‑1 (MQ=255)

                                                                                                gtgtCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCCCtt                                     >  2:246113/1‑141 (MQ=255)

                                                                                                gtgtCTAACAACAATGGTATTATTTTCCTTAATATATGAAGCTTTTGTCAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACtt                                     <  2:227626/141‑1 (MQ=255)

                                                                                                             aTGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTATTaaaa                        >  2:170405/1‑141 (MQ=255)

                                                                                                               ggTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa                      <  1:26733/141‑1 (MQ=255)

                                                                                                                  attattTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATgg                   >  2:122781/1‑141 (MQ=255)

                                                                                                                   ttattTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGt                  >  1:281519/1‑141 (MQ=255)

                                                                                                                     attTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTATGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGa                <  2:170579/141‑1 (MQ=255)

                                                                                                                       tttCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAg              <  1:24267/141‑1 (MQ=255)

                                                                                                                          ccTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGtaa           >  2:76671/1‑139 (MQ=255)

                                                                                                                                   ttGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAt  <  1:246113/141‑1 (MQ=255)

TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAT  >  USA300TCH1516_ALE/2028057‑2028328

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