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 F2 I1 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	Exported	217,959	A→G	20.6%	intergenic (‑51/‑55)	yafU ← / → yafF	predicted inner membrane protein/conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	217,959	0	A	G	20.6%	313.6 / 75.7	160	intergenic (‑51/‑55)	yafU/yafF	predicted inner membrane protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (49/78); new base G (15/18); total (64/96)
Fisher's exact test for biased strand distribution p-value = 5.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 163 total aligned reads displayed.

GATCTCGCTCTGAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGA  >  Exported/217890‑218027

gATCTCGCTCTGAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCaa                                                                     <  1:4370313/71‑1 (MQ=255)

      gCTCCGAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGa                                                                <  1:4354214/70‑1 (MQ=255)

            aaCTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCAc                                                          <  1:2669981/70‑1 (MQ=255)

                    ataaATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTg                                                 >  1:1605096/1‑71 (MQ=255)

                    ataaATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTg                                                 <  1:1512108/71‑1 (MQ=255)

                        aTTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGa                                                                <  1:486304/52‑1 (MQ=255)

                        aTTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGa                                                                <  1:1485011/52‑1 (MQ=255)

                             tcagTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGATAATAAg                                        <  1:914249/68‑1 (MQ=255)

                             tcagTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAg                                        <  1:701778/68‑1 (MQ=255)

                              tGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATa                                          <  1:2511962/68‑1 (MQ=255)

                              cagTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGa                                                                <  1:1747627/44‑1 (MQ=37)

                              cagTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTg                                                        >  1:2283110/3‑54 (MQ=255)

                                gTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTg                                     <  1:2634944/71‑1 (MQ=255)

                                gTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCt                                      >  1:3081042/1‑70 (MQ=255)

                                gTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATaa                                         <  1:4777835/67‑1 (MQ=255)

                                gTTCTGCTGATTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTg                                     >  1:5045809/1‑71 (MQ=255)

                                 ttCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCAc                                                          <  1:2789026/49‑1 (MQ=255)

                                   ctgctgATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCAc                                                          >  1:4101966/1‑47 (MQ=25)

                                   ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGcac                                  >  1:346636/1‑71 (MQ=255)

                                   ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                   <  1:1709404/70‑1 (MQ=255)

                                   ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                   <  1:2322516/70‑1 (MQ=255)

                                   ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                   <  1:3278884/70‑1 (MQ=255)

                                   ctgctgATTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGcac                                  >  1:4592529/1‑71 (MQ=255)

                                   ctgctgATTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGcac                                  >  1:775220/1‑71 (MQ=255)

                                    tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                     <  1:3371385/67‑1 (MQ=255)

                                    tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                     <  1:2292927/67‑1 (MQ=255)

                                    tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGCCATGTGGAGAATAAGCTg                                     <  1:1386567/67‑1 (MQ=255)

                                     gctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGa                                                                <  1:1060539/39‑1 (MQ=255)

                                     gctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGaa                                            <  1:888866/59‑1 (MQ=255)

                                      ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCa                                                           >  1:5249360/1‑43 (MQ=255)

                                      ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTgg                                                       >  1:3438182/1‑47 (MQ=255)

                                      ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTga                                                       >  1:5483034/1‑46 (MQ=255)

                                      ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGcac                                  <  1:2223114/68‑1 (MQ=255)

                                      ctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTAGCATGTGGAGAATAAGCTGCACTgg                               >  1:5356633/1‑71 (MQ=255)

                                      ctgATTTAACCGCAGAAAAGTTCGCCACAGCAATCCg                                                                 <  1:5199602/37‑1 (MQ=255)

                                         aTTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAg                                        >  1:2922580/1‑59 (MQ=255)

                                         aTTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCAc                                                          >  1:1075564/1‑41 (MQ=255)

                                         aTTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTgg                                                       <  1:2494219/44‑1 (MQ=255)

                                         aTTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                            >  1:4721210/1‑71 (MQ=255)

                                         aTTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGc                              <  1:4158700/69‑1 (MQ=255)

                                          tttAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTc                           >  1:3650968/1‑71 (MQ=255)

                                           ttAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACg                                                   >  1:1863310/1‑46 (MQ=25)

                                           ttAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCt                          >  1:456631/1‑71 (MQ=255)

                                           ttAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGt                            >  1:3662270/1‑69 (MQ=255)

                                            tAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCt                          <  1:1294206/70‑1 (MQ=255)

                                            tAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                       >  1:4052539/1‑57 (MQ=255)

                                            tAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTg                         >  1:1009297/1‑71 (MQ=255)

                                             aaCCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                         <  1:2028959/70‑1 (MQ=255)

                                             aaCCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                         <  1:1689379/70‑1 (MQ=255)

                                             aaCCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                         <  1:3691445/70‑1 (MQ=255)

                                              aCCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                         <  1:1220340/69‑1 (MQ=255)

                                               ccGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGcac                                  <  1:789490/59‑1 (MQ=255)

                                                cGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACg                     <  1:4357549/71‑1 (MQ=255)

                                                cGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGgag                                              <  1:2625925/46‑1 (MQ=255)

                                                cGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGgag                                              <  1:3727569/46‑1 (MQ=255)

                                                  ctgagaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAg                                        >  1:2269167/3‑50 (MQ=37)

                                                  ctgagaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTg                   >  1:1464334/3‑71 (MQ=255)

                                                  cAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGcactg                                <  1:5480294/58‑3 (MQ=255)

                                                  cAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                   >  1:316088/1‑55 (MQ=255)

                                                   agagAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTgg                                                <  1:318990/41‑1 (MQ=255)

                                                   agagAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTgg                                                <  1:1701365/41‑1 (MQ=255)

                                                    gaaaaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                 <  1:1425037/68‑1 (MQ=255)

                                                     agaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                 <  1:5014862/70‑1 (MQ=255)

                                                      gaAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaa               >  1:5564911/1‑71 (MQ=255)

                                                      gaAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaa               <  1:4244904/71‑1 (MQ=255)

                                                       aaattCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACg                     <  1:2987081/61‑1 (MQ=255)

                                                       aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat              <  1:4857679/71‑1 (MQ=255)

                                                       aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat              >  1:3358243/1‑71 (MQ=255)

                                                       aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat              >  1:2452531/1‑71 (MQ=255)

                                                       aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                       >  1:1007590/1‑46 (MQ=255)

                                                       aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                       >  1:3090713/1‑46 (MQ=255)

                                                        aGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat              <  1:4325223/70‑1 (MQ=255)

                                                        aGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg             <  1:844892/71‑1 (MQ=255)

                                                        aGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg             <  1:231813/71‑1 (MQ=255)

                                                         attCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg             >  1:3880512/2‑70 (MQ=255)

                                                          ttCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGca                                   >  1:3931760/1‑47 (MQ=255)

                                                          ttCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGca                                   >  1:5407114/1‑47 (MQ=255)

                                                            cGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaat          >  1:4831018/1‑70 (MQ=255)

                                                            cGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaat          >  1:3005613/1‑70 (MQ=255)

                                                             gCCACAGCAATCCGAAACCTCTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAatgaatga        <  1:4296141/71‑1 (MQ=255)

                                                              ccACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa       <  1:3373769/71‑1 (MQ=255)

                                                              ccACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa       <  1:2614983/71‑1 (MQ=39)

                                                              ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa       <  1:479102/71‑1 (MQ=255)

                                                              ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa       <  1:949904/71‑1 (MQ=255)

                                                              ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAAtgaatgaa       <  1:2137598/71‑1 (MQ=255)

                                                               cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACg                     >  1:258264/1‑56 (MQ=38)

                                                               cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa           <  1:2563555/66‑1 (MQ=39)

                                                               cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa           <  1:3630250/66‑1 (MQ=39)

                                                               cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa           <  1:3734292/66‑1 (MQ=39)

                                                               cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa           <  1:211418/66‑1 (MQ=39)

                                                               cacaGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTg                         <  1:1440846/52‑1 (MQ=255)

                                                                acaGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAga     >  1:1180948/1‑71 (MQ=255)

                                                                 caGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac    >  1:2921521/1‑71 (MQ=255)

                                                                 caGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac    <  1:1755055/71‑1 (MQ=255)

                                                                  aGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTc                           <  1:3297961/47‑1 (MQ=255)

                                                                  aGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacg   <  1:2897789/71‑1 (MQ=255)

                                                                   gCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgacga  >  1:2762749/1‑71 (MQ=255)

                                                                    cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa           <  1:93979/61‑1 (MQ=38)

                                                                    cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa       <  1:1723496/65‑1 (MQ=39)

                                                                    cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa       <  1:153989/65‑1 (MQ=39)

GATCTCGCTCTGAACTCATAATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGA  >  Exported/217890‑218027

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A