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 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,257,455 C→T 74.0% G9R (GGA→AGA)  yeiJ ← predicted nucleoside transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,257,4550CT74.0% 130.5 / 52.2 77G9R (GGA→AGA) yeiJpredicted nucleoside transporter
Reads supporting (aligned to +/- strand):  ref base C (4/16);  new base T (23/34);  total (27/50)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GGTACGCAGGCTGATCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCTTTCTGC  >  W3110S.gb/2257387‑2257521
                                                                    |                                                                  
ggaaCGCAGGCTGATCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTcc                                                                    >  1:495673/4‑69 (MQ=255)
 gTACGCAGGCTGATCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAg                                                                 <  1:2313041/71‑1 (MQ=255)
           tGATCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACtt                                                          >  1:1269752/1‑68 (MQ=255)
             aTCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAaca                                                             <  1:1609742/63‑1 (MQ=255)
             aTCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAaca                                                             <  1:462609/63‑1 (MQ=255)
               cttcttcttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGa                                                   >  1:2549514/1‑71 (MQ=255)
               cttcttcttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGa                                                   >  1:2093828/1‑71 (MQ=255)
               cttcttcttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGa                                                   >  1:855632/1‑71 (MQ=255)
               cttcttcttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGa                                                   >  1:1066424/1‑71 (MQ=255)
                  cttcttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATg                                                    <  1:213658/67‑1 (MQ=255)
                     cttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTGTCAGAACACTTCTCATGACATc                                               <  1:2109973/69‑1 (MQ=255)
                     cttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATc                                               <  1:1620876/69‑1 (MQ=255)
                     cttGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATc                                               <  1:278047/69‑1 (MQ=255)
                        gTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCAt                                            <  1:1662614/69‑1 (MQ=255)
                        gTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCAt                                            <  1:959097/69‑1 (MQ=255)
                         tttACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGt                                         <  1:2211362/71‑1 (MQ=255)
                         tttACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGt                                         <  1:524924/71‑1 (MQ=255)
                         tttACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCATAGt                                         <  1:711486/71‑1 (MQ=255)
                            agtGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGAt                                      >  1:324743/3‑71 (MQ=255)
                             cTGACAGTAAAAACGCAATCGTCTGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGAtt                                     <  1:2189758/71‑1 (MQ=255)
                             cTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGAt                                      <  1:1464738/70‑1 (MQ=255)
                             cTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGAt                                      <  1:2262326/70‑1 (MQ=255)
                             cTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGAt                                      <  1:2140735/70‑1 (MQ=255)
                               gACAGTAAAAACGCAATCGTCAGCAATACCCCCATTCCCAGaa                                                               >  1:2602988/1‑43 (MQ=255)
                                   gTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCAt                                                     <  1:2548013/49‑1 (MQ=255)
                                   gTAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATa                                           <  1:741360/59‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTtctc                                                       <  1:1512558/46‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTtctc                                                       <  1:2696946/46‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTtctc                                                       <  1:2688764/46‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGa                                                   >  1:2413484/1‑50 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGa                                                   >  1:1196106/1‑50 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGa                                                   >  1:2362106/1‑50 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGa                                                   >  1:1060807/1‑50 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCtt                              <  1:1033828/71‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTtct                                                        <  1:520036/45‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCAt                                                     <  1:127537/48‑1 (MQ=255)
                                    tAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCtt                              <  1:2375861/71‑1 (MQ=255)
                                    tAAAAACGCAATCGGCAGCAATACCACCATTCCCAGAACACTtct                                                        <  1:2319773/45‑1 (MQ=255)
                                     aaaaaCGCAATCGTCAGCAATACCACCATTCTGAGaa                                                               >  1:366490/1‑37 (MQ=38)
                                     aaaaaCGCAATCGTCAGCAATACCACCATTCTCAGaa                                                               >  1:1405899/1‑37 (MQ=255)
                                     aaaaaCGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGt                                         >  1:475375/1‑59 (MQ=255)
                                     aaaaaCGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCtt                              >  1:2682261/1‑70 (MQ=255)
                                     aaaaaCGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCAt                                                     <  1:2809552/47‑1 (MQ=255)
                                      aaaaCGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTc                             <  1:1835426/70‑1 (MQ=255)
                                      aaaaCGCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCa                            >  1:2310906/1‑71 (MQ=255)
                                      aaaaCGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCa                            <  1:1172348/71‑1 (MQ=255)
                                       aaaCGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCtt                              <  1:2134358/68‑1 (MQ=255)
                                           gCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       <  1:2770660/71‑1 (MQ=255)
                                           gCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       <  1:2243476/71‑1 (MQ=255)
                                           gCAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       <  1:213290/71‑1 (MQ=255)
                                            cAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCat                      <  1:2469799/71‑1 (MQ=255)
                                            cAATCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCat                      <  1:441323/71‑1 (MQ=255)
                                               tCGTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTAtc                                  <  1:698942/56‑1 (MQ=255)
                                                 gTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTgg                 >  1:541290/1‑71 (MQ=255)
                                                 gTCAGCAATACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTg                  >  1:113666/1‑70 (MQ=255)
                                                        aTACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGc               <  1:1160307/66‑1 (MQ=255)
                                                         tACCACCATTCTCAGAACACTTCTCATGACATCCa                                             <  1:1471465/35‑1 (MQ=255)
                                                         tACCACCATTCTCAGAACACTTCTCATGACATCCAt                                            <  1:1037734/36‑1 (MQ=255)
                                                         tACCACCATTCTCAGAACACTTCTCATGACATCCAt                                            <  1:1306101/36‑1 (MQ=255)
                                                         tACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       <  1:1679889/57‑1 (MQ=255)
                                                         tACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       <  1:2170886/57‑1 (MQ=255)
                                                         tACCACCATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       <  1:1319672/57‑1 (MQ=255)
                                                         tACCACCATTCCCAGAACACTTCTCATGACATCCATAGTTATTATCTCTTCATGTCATATTGGGc               <  1:1919982/65‑1 (MQ=255)
                                                          accaccATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCa                            >  1:2208833/1‑51 (MQ=255)
                                                          accaccATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGa             >  1:1642357/1‑66 (MQ=255)
                                                          accaccATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCt        >  1:1244037/1‑71 (MQ=255)
                                                          accaccATTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCt        >  1:1346863/1‑71 (MQ=255)
                                                           ccaccaTTCTCAGAACACTTCTCATGACATCCATAg                                          >  1:593220/1‑36 (MQ=255)
                                                           ccaccaTTCTCAGAACACTTCTCATGACATCCATAGTGAt                                      <  1:1742355/40‑1 (MQ=255)
                                                           ccaccaTTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTg                  >  1:786267/1‑60 (MQ=255)
                                                           ccaccaTTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCtt       >  1:807529/1‑71 (MQ=255)
                                                           ccaccaTTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCt        <  1:1039937/70‑1 (MQ=255)
                                                           ccaccaTTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCat                      <  1:1647200/56‑1 (MQ=255)
                                                           ccaccaTTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCa                       >  1:2739199/1‑55 (MQ=255)
                                                            caccaTTCCCAGAACACTTCTCATGACATCCATAGTGATTAtctc                                <  1:2316271/45‑1 (MQ=255)
                                                             accaTTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCTTTc     <  1:587574/71‑1 (MQ=255)
                                                                aTTCTCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCTTTCTGc  >  1:2089029/1‑71 (MQ=255)
                                                                 ttCTCAGAACACTTCTCATGACATCCATAGTGATTAtctc                                <  1:173152/40‑1 (MQ=255)
                                                                   cccAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCTTTc     >  1:2345475/1‑65 (MQ=255)
                                                                   cccAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCTTTc     >  1:577805/1‑65 (MQ=255)
                                                                    |                                                                  
GGTACGCAGGCTGATCTTCTTCTTGTTTACTGACAGTAAAAACGCAATCGTCAGCAATACCACCATTCCCAGAACACTTCTCATGACATCCATAGTGATTATCTCTTCATGTCATATTGGGCGACGGCTTTCTGC  >  W3110S.gb/2257387‑2257521

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A