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
A14 F1 I1 R1	71	51.6	2219666	95.9%	2128659	118.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,532,523	(A)_7→8	intergenic (‑84/‑295)	yhgE ← / → pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP]

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,532,516	1	.	A	98.0%	175.5 / ‑3.4	51	intergenic (‑77/‑302)	yhgE/pck	DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP]
Reads supporting (aligned to +/- strand): ref base . (0/1); new base A (24/26); total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01

ATCATCCCCCAGCGTGTTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATC‑AAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAACCAAGATTTAACCTTTTGAGAACATTTTCCAC  >  NC_000913/3532396‑3532646

atcatcCCCCAGCGTGTTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCgtgg                                                                                                                   <  1:921541/139‑1 (MQ=255)

  catcCCCCAGCGTGTTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCgtggtg                                                                                                                 <  1:803656/139‑1 (MQ=255)

         cAGCGTGTTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGAt                                                                                                          >  2:612391/1‑139 (MQ=255)

               gtTGCGGTTGAAAGTTCAACGTTATCCATTTTGTTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTa                                                                                                    <  1:830962/139‑1 (MQ=255)

               gtTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTATTTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTa                                                                                                    <  1:672761/139‑1 (MQ=255)

               gtTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTa                                                                                                    <  1:980864/139‑1 (MQ=255)

                ttGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTAc                                                                                                   >  1:1065409/1‑139 (MQ=255)

                ttGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTAc                                                                                                   >  2:1084879/1‑139 (MQ=255)

                          aaGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAAtt                                                                                         <  1:775127/139‑1 (MQ=255)

                                aaCGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTAc                                                                                                   >  1:406432/1‑123 (MQ=255)

                                aaCGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTAc                                                                                                   <  2:406432/123‑1 (MQ=255)

                                       tCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATttca                                                                            >  1:902921/1‑139 (MQ=255)

                                            gTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAg                                                                       >  2:237392/1‑139 (MQ=255)

                                            gTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAg                                                                       >  2:92006/1‑139 (MQ=255)

                                              tGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGa                                                                     <  2:358163/139‑1 (MQ=255)

                                               ggTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGaa                                                                    >  1:139820/1‑139 (MQ=255)

                                                 ttATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATg                                                                  >  2:18980/1‑139 (MQ=255)

                                                 ttATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATg                                                                  >  1:410162/1‑139 (MQ=255)

                                                       aGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTc                                                            <  1:831926/139‑1 (MQ=255)

                                                       aGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTc                                                            <  2:266669/139‑1 (MQ=255)

                                                        gAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTcc                                                           >  1:287937/1‑139 (MQ=255)

                                                         aaTCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAg                                                                       <  1:910320/126‑1 (MQ=255)

                                                         aaTCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAg                                                                       >  2:910320/1‑126 (MQ=255)

                                                          aTCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCAc                                                         <  2:287937/139‑1 (MQ=255)

                                                          aTCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCAc                                                         >  2:877379/1‑139 (MQ=255)

                                                           tCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACt                                                        <  2:410162/139‑1 (MQ=255)

                                                           tCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACt                                                        <  1:1084879/139‑1 (MQ=255)

                                                              aaaGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTcac                                                     >  1:597371/1‑139 (MQ=255)

                                                                aGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACaa                                                   >  2:684365/1‑139 (MQ=255)

                                                                     ggTTAATTATCGCATCCGGGCGGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTc                                              >  1:230409/1‑139 (MQ=255)

                                                                     ggTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTc                                              >  2:391821/1‑139 (MQ=255)

                                                                     ggTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTc                                              >  2:927889/1‑139 (MQ=255)

                                                                        tAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCg                                           <  1:593685/139‑1 (MQ=255)

                                                                        tAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCg                                           <  1:25605/139‑1 (MQ=255)

                                                                        tAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCg                                           <  2:892561/139‑1 (MQ=255)

                                                                            tATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCAc                                                         <  2:1040814/121‑1 (MQ=255)

                                                                            tATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCAc                                                         >  1:1040814/1‑121 (MQ=255)

                                                                            tATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCat                                       <  1:237392/139‑1 (MQ=255)

                                                                            tATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATC‑AAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCata                                      <  1:976713/139‑1 (MQ=255)

                                                                             aTCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCata                                      >  2:656057/1‑139 (MQ=255)

                                                                                   tCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAAcc                                >  1:617074/1‑139 (MQ=255)

                                                                                   tCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAAcc                                <  1:1083345/139‑1 (MQ=255)

                                                                                     cGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAAtt                                                                                         >  1:86916/1‑80 (MQ=255)

                                                                                     cGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAAtt                                                                                         <  2:86916/80‑1 (MQ=255)

                                                                                       ggCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCg                                           >  2:143757/1‑124 (MQ=255)

                                                                                       ggCAGTAGTATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCg                                           <  1:143757/124‑1 (MQ=255)

                                                                                          agtagtATTTTGCTTTTTTCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAACCAAGAttt                         <  1:18980/139‑1 (MQ=255)

                                                                                                         ttttCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCAt                                                                                    <  2:1097426/65‑1 (MQ=255)

                                                                                                         ttttCAGAAAATAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCAt                                                                                    >  1:1097426/1‑65 (MQ=255)

                                                                                                                aaaaTAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAACCAAGATTTAACCTTTTGAGAACATTTTCca   <  1:92006/139‑1 (MQ=255)

                                                                                                                 aaaTAATCAAAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAACCAAGATTTAACCTTTTGAGAACATTTTCcac  <  2:968057/139‑1 (MQ=255)

ATCATCCCCCAGCGTGTTGCGGGTGAAAGTTCAACGTTATCCATGTTGGTTATCCAGAATCAAAAGGTGGGTTAATTATCGCATCCGGGCAGTAGTATTTTGCTTTTTTCAGAAAATAATC‑AAAAAAAGTTAGCGTGGTGAATCGATACTTTACCGGTTGAATTTGCATCAATTTCATTCAGGAATGCGATTCCACTCACAATATTCCCGCCATATAAACCAAGATTTAACCTTTTGAGAACATTTTCCAC  >  NC_000913/3532396‑3532646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A