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 F56 I0 R1	19	43.9	998620	94.5%	943695	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,191	C→A	72.7%	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	72.7%	47.5 / 14.8	34	A152S (GCA→TCA)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (2/7); new base A (12/12); total (14/20)
Fisher's exact test for biased strand distribution p-value = 2.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAT  >  USA300TCH1516_ALE/2028057‑2028328

tGATTTTTCATTCACGTAAGTACGTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCttt                                                                                                                                     <  1:421662/141‑1 (MQ=255)

   tttttCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGt                                                                                                                                  <  1:199959/141‑1 (MQ=255)

         attcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTc                                                                                                                            >  2:18801/1‑141 (MQ=255)

         attcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTc                                                                                                                            <  2:475444/141‑1 (MQ=255)

          ttcaCGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTATACCAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCa                                                                                                                           >  1:469984/1‑141 (MQ=255)

           tcaCGTAAGTACTACCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATGTGAAGCTTTTGTTACGTCaa                                                                                                                          >  2:357790/1‑141 (MQ=255)

                 aaGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATCGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTACCAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCACTCTGTa                                                                                                                    >  2:183528/1‑141 (MQ=255)

                  aGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAg                                                                                                                   >  1:449782/1‑141 (MQ=255)

                      tttCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAGCTGTACTTTACCTAAAATGTGTCTAACTACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCg                                                                                                               <  2:117283/140‑1 (MQ=255)

                      cTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCg                                                                                                               >  1:419875/1‑141 (MQ=255)

                        tCCACAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGcc                                                                                                             <  1:13480/141‑1 (MQ=255)

                             aaaaaGCAGCTAAATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTc                                                                                                        >  2:62802/1‑141 (MQ=255)

                              aaaaGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTcc                                                                                                       <  1:140994/141‑1 (MQ=255)

                                 agcagcTACATGTAAATTAATATTGTAAGTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATGTGCAGGTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATg                                                                                                    <  2:169359/141‑1 (MQ=255)

                                               aaTTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGATGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCTATGTTGAATTTGTACAt                                                                                      <  2:84868/141‑1 (MQ=255)

                                                 ttAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTATAATGTTTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCt                                                                                    <  1:162244/141‑1 (MQ=255)

                                                     tagtttAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTccc                                                                                <  2:121769/136‑1 (MQ=255)

                                                                aCCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTAAATCCGCCCACTTATATACa                                                                     >  2:323182/1‑141 (MQ=255)

                                                                  cGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATa                                                                   >  1:64192/1‑141 (MQ=255)

                                                                    gCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGCAGCATTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTAAATCTTCCCACTTATATACATaaa                                                                 >  2:340435/1‑141 (MQ=255)

                                                                      aaTATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACt                                                               <  1:204961/141‑1 (MQ=255)

                                                                        tataACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTgg                                                             >  1:317315/1‑141 (MQ=255)

                                                                                 cACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTg                                                    >  2:410306/1‑141 (MQ=255)

                                                                                  aCTTTACCTAAAATGTGTCTAACCACAATGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGc                                                   <  1:134188/141‑1 (MQ=255)

                                                                                  aCTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTGTATACATAAACTGGTGTACGTTGc                                                   <  1:96392/141‑1 (MQ=255)

                                                                                      tACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCAc                                               <  2:422158/141‑1 (MQ=255)

                                                                                            aaaTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTTGAGCTTTTGTTAAGTGAATATGTAGGTCGCGAATTCGATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAAcc                                         <  2:125690/141‑1 (MQ=255)

                                                                                             aaTGTGTCTAACAACAATGGTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCa                                        >  1:189970/1‑141 (MQ=255)

                                                                                                          acaaTGGTATTATTTTCCTTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTGGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTtaata                           <  1:18801/141‑1 (MQ=255)

                                                                                                               ggTATTATTTTCCTTAATATTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGa                      >  2:271347/1‑141 (MQ=255)

                                                                                                                  tttattTTCCGTAATATTTGCAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATgg                   <  2:468413/140‑1 (MQ=255)

                                                                                                                                tatTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCt     <  1:168592/141‑1 (MQ=255)

                                                                                                                                tatTTGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCt     <  1:431071/141‑1 (MQ=255)

                                                                                                                                   ttGAAGCTTTTGTTAAGTCAATATGTAGGTCGCCAATTCCATGTTGAATTTGTACATCTTCCCACTTATATACATAAACTGGTGTACGTTGCTCACCAAACCACTTTTGTTTAATAAAAGATGGTGAAGTCATAACCTCAt  <  2:419875/141‑1 (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