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 217,977 C→T 31.9% intergenic (‑69/‑37) 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
*Exported217,9770CT31.9% 246.1 / 154.9 194intergenic (‑69/‑37)yafU/yafFpredicted inner membrane protein/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (60/72);  new base T (24/38);  total (84/110)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

Only 100 of 195 total aligned reads displayed.

ATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGA  >  Exported/217910‑218043
                                                                   |                                                                  
         tcagTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGATAATAAg                                                        <  1:914249/68‑1 (MQ=255)
          tGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATa                                                          <  1:2511962/68‑1 (MQ=255)
          cagTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGc                                                       >  1:1800812/3‑71 (MQ=255)
            gTTCTGCTGATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTg                                                     <  1:2634944/71‑1 (MQ=255)
            gTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCt                                                      >  1:3081042/1‑70 (MQ=255)
            gTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                                     <  1:1500413/71‑1 (MQ=255)
            gTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATaa                                                         <  1:4777835/67‑1 (MQ=255)
              tCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                                       >  1:2127757/1‑67 (MQ=255)
               ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                                   <  1:1709404/70‑1 (MQ=255)
               ctgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGca                                                   <  1:3278884/70‑1 (MQ=255)
               ctgctgATTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGcac                                                  >  1:775220/1‑71 (MQ=255)
               ctgctgATTTAACCGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGcac                                                  >  1:4592529/1‑71 (MQ=255)
                tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                                     <  1:3364865/67‑1 (MQ=255)
                tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                                     <  1:2292927/67‑1 (MQ=255)
                tgctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGCCATGTGGAGAATAAGCTg                                                     <  1:1386567/67‑1 (MQ=255)
                 gctgATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGaa                                                            <  1:888866/59‑1 (MQ=255)
                    gATTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGcactg                                                <  1:2472351/68‑3 (MQ=255)
                     aTTTAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAg                                                        >  1:2922580/1‑59 (MQ=255)
                     aTTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                            >  1:4721210/1‑71 (MQ=255)
                       ttAACCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACg                                                                   >  1:1863310/1‑46 (MQ=25)
                       ttAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGt                                            >  1:3662270/1‑69 (MQ=255)
                        tAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                                         >  1:2033247/1‑71 (MQ=255)
                         aaCCGCTGAGAAATTCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTg                                         <  1:3691445/70‑1 (MQ=255)
                          aCCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                                         <  1:1220340/69‑1 (MQ=255)
                           ccGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGcac                                                  <  1:789490/59‑1 (MQ=255)
                            cGCAGAAAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGgag                                                              <  1:3727569/46‑1 (MQ=255)
                             gCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGt                                    <  1:320840/71‑1 (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)
                               agagAAGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTg                                                     <  1:4280936/52‑1 (MQ=255)
                               agagAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTgg                                  <  1:5525763/71‑1 (MQ=255)
                                gaaaaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGt                                 <  1:1425037/68‑1 (MQ=255)
                                 aaaaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATaa                                                         <  1:3403752/44‑1 (MQ=255)
                                  gaAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaa                               >  1:5564911/1‑71 (MQ=255)
                                  aaaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAg                                                        >  1:4014494/2‑46 (MQ=255)
                                   aaattCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACg                                     <  1:2987081/61‑1 (MQ=255)
                                   aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTg                                         <  1:1060063/60‑1 (MQ=38)
                                   aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACg                                     <  1:2818678/64‑1 (MQ=255)
                                   aaGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                              <  1:4857679/71‑1 (MQ=255)
                                   aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                                       >  1:3090713/1‑46 (MQ=255)
                                   aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGc                                                       >  1:1007590/1‑46 (MQ=255)
                                   aaGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaa                               >  1:4839950/1‑70 (MQ=255)
                                    aGTTCGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                              <  1:4325223/70‑1 (MQ=255)
                                    aGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTaatg                             <  1:231813/71‑1 (MQ=255)
                                     attCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATa                                                          <  1:2619449/40‑1 (MQ=38)
                                     attCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                             >  1:3880512/2‑70 (MQ=255)
                                      ttCGCCACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGca                                                   >  1:4806457/1‑47 (MQ=255)
                                        cGCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaat                          >  1:408426/1‑70 (MQ=39)
                                         gCCACAGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaatg                         >  1:4191845/1‑70 (MQ=39)
                                         gCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                             <  1:1666448/66‑1 (MQ=255)
                                         gCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatg                             <  1:1526480/66‑1 (MQ=255)
                                          ccACAGCGATCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:3373769/71‑1 (MQ=255)
                                          ccACAGCAATCCGAAACCACTGGCACGTGGATAATAAGCTGCACAGGCGTCTGGACGt                                    <  1:1691448/58‑1 (MQ=255)
                                          ccACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:949904/71‑1 (MQ=255)
                                           cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACg                                     >  1:258264/1‑56 (MQ=38)
                                           cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                           <  1:3630250/66‑1 (MQ=39)
                                           cacaGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                           <  1:2563555/66‑1 (MQ=39)
                                            acaGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAga                     >  1:1180948/1‑71 (MQ=255)
                                             caGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac                    <  1:1755055/71‑1 (MQ=255)
                                              aGCAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAatgaatga                        >  1:5182723/1‑66 (MQ=39)
                                               gcgaTCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                  <  1:1558165/68‑1 (MQ=255)
                                               gCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                  >  1:5384363/1‑71 (MQ=255)
                                               gCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgacga                  >  1:2762749/1‑71 (MQ=255)
                                                cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaatgaa                           <  1:93979/61‑1 (MQ=38)
                                                cAATCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:1723496/65‑1 (MQ=39)
                                                cAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                  <  1:4896869/70‑1 (MQ=255)
                                                 aaTCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCg                                             <  1:3353800/42‑1 (MQ=255)
                                                  aTCCGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTgg                                  <  1:2915520/52‑1 (MQ=255)
                                                  aTCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgac                    <  1:5408078/66‑1 (MQ=255)
                                                   tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                            <  1:5121478/41‑1 (MQ=25)
                                                   tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGt                                            <  1:4398494/41‑1 (MQ=25)
                                                   tCCGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACtg               >  1:3170285/1‑69 (MQ=39)
                                                   tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgac                    <  1:1304847/65‑1 (MQ=255)
                                                   tCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGt                                            <  1:1212738/41‑1 (MQ=255)
                                                    ccGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       >  1:2423762/1‑61 (MQ=255)
                                                    ccGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       >  1:2045651/1‑61 (MQ=255)
                                                    ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:4957015/61‑1 (MQ=255)
                                                    ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTAc              >  1:3945071/1‑70 (MQ=255)
                                                    ccGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTAc              >  1:3331895/1‑70 (MQ=255)
                                                     cGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:2216808/60‑1 (MQ=255)
                                                     cGAAATCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:349716/60‑1 (MQ=255)
                                                     cGAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCa             >  1:3812282/1‑70 (MQ=38)
                                                     cGAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCa             >  1:3648158/1‑70 (MQ=255)
                                                      gAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                  >  1:5029932/1‑64 (MQ=255)
                                                      gAAACCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAgacga                  >  1:85915/1‑64 (MQ=255)
                                                      gAAACCACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAAtgaatgaa                       <  1:1950028/59‑1 (MQ=255)
                                                       aaaCCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACaaaa          >  1:1000416/1‑71 (MQ=255)
                                                         atcACTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAAt         >  1:4553976/3‑70 (MQ=255)
                                                         aCCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCaaaa          >  1:716916/1‑69 (MQ=39)
                                                         aCCACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAAt         >  1:4678397/1‑70 (MQ=255)
                                                          ccACTGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGt                                    <  1:2369899/42‑1 (MQ=37)
                                                            aCTGGCACGTGGAGAATAAGCTGCACTGGCGTCTggc                                       >  1:2237848/1‑36 (MQ=39)
                                                            aCTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaag      >  1:1143779/1‑70 (MQ=255)
                                                            aCTGGCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTAATGAATGAAGACGACTGCAAAATaag      >  1:1612584/1‑70 (MQ=255)
                                                              tGGCATGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaat                              <  1:2861152/44‑1 (MQ=38)
                                                              tGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAgac                    <  1:68454/54‑1 (MQ=255)
                                                                gCACGTGGAGAATAAGCTGCACTGGCGTCTGGACGTGGTaa                               >  1:3668275/1‑41 (MQ=255)
                                                                gCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAagaaga  <  1:5262444/70‑1 (MQ=255)
                                                                   |                                                                  
ATAAATTCTATGGTTCTGCTGATTTAACCGCAGAGAAGTTCGCCACAGCAATCCGAAACCACTGGCACGTGGAGAATAAGCTGCACAGGCGTCTGGACGTGGTAATGAATGAAGACGACTACAAAATAAGAAGA  >  Exported/217910‑218043

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A