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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,449,567 C→T 15.8% V17I (GTT→ATT)  yfcL ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,449,5670CT15.8% 193.8 / 25.1 76V17I (GTT→ATT) yfcLhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/39);  new base T (8/4);  total (33/43)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

ATGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTAAAAC  >  W3110S.gb/2449500‑2449636
                                                                   |                                                                     
aTGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGTCATGGTCAACCa                                                                     <  1:1028628/70‑1 (MQ=255)
aTGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAAc                                                                       >  1:2065050/1‑68 (MQ=255)
aTGGCTAATGTCAGGTGGCAACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCa                                                                     >  1:1049766/1‑70 (MQ=255)
 tGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                    <  1:2070998/70‑1 (MQ=255)
       aTGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTc                                                              <  1:3885866/70‑1 (MQ=255)
       aTGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTc                                                              <  1:1113764/70‑1 (MQ=255)
          tCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAt                                                           >  1:869980/1‑70 (MQ=255)
                ggCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGc                                                     >  1:1293746/1‑70 (MQ=255)
                 gCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGAtt                                                          <  1:630204/64‑1 (MQ=255)
                 gCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGcc                                                    <  1:1297667/70‑1 (MQ=255)
                  ccACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                                  <  1:4405643/71‑1 (MQ=255)
                  ccACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                                  <  1:1616216/71‑1 (MQ=255)
                   cACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATAGCGTCGATTaa                                                        >  1:2031790/1‑64 (MQ=255)
                   cACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                                  >  1:4349820/1‑70 (MQ=255)
                       cAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCATAATGc                                             >  1:4452929/1‑71 (MQ=255)
                       cAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATg                                              >  1:4022408/1‑70 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGt                                           <  1:4141337/71‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGt                                           <  1:3760510/71‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGt                                           <  1:4623847/71‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGt                                           <  1:4062734/71‑1 (MQ=255)
                         aaTACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGt                                           >  1:775339/1‑71 (MQ=255)
                           tACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTaa                                                        >  1:1359569/1‑56 (MQ=255)
                           tACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                    <  1:151148/44‑1 (MQ=255)
                           tACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCAt                                                                    <  1:3042291/44‑1 (MQ=255)
                           tACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATAc                                                                  >  1:2230136/1‑46 (MQ=255)
                           tACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAAt                                               >  1:4437082/1‑65 (MQ=255)
                            aCCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGa                                                            >  1:1193909/1‑51 (MQ=255)
                            aCCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGc                                                     >  1:2683276/1‑58 (MQ=255)
                               cACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                     <  1:681102/71‑1 (MQ=255)
                               cACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                     <  1:2190951/71‑1 (MQ=255)
                                aCTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGa                                                            >  1:2892285/1‑47 (MQ=255)
                                aCTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGa                                                            >  1:1779292/1‑47 (MQ=255)
                                aCTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGaa                                                >  1:2442149/1‑59 (MQ=255)
                                aCTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTc                                      >  1:2769543/1‑69 (MQ=255)
                                 cTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCaaa                                   <  1:3142057/71‑1 (MQ=255)
                                  tGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                          <  1:4199306/47‑1 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACt                                 >  1:4070352/1‑71 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCTATTAATGCCAGAATg                                              <  1:147883/58‑1 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                          <  1:1953009/46‑1 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTa                                                         >  1:24403/1‑47 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTa                                                         >  1:1695486/1‑47 (MQ=255)
                                   ggCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                                  <  1:1832841/54‑1 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAATCATAc                                                                  >  1:1884346/1‑37 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGa                                                            >  1:267604/1‑43 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCaaa                                   <  1:117273/68‑1 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTc                                >  1:2534421/1‑71 (MQ=255)
                                    gCAAACAACTCATCATCACTGGCATGGGCAACCATACCGTCGAtt                                                          <  1:2329437/45‑1 (MQ=255)
                                      aaaCAACTCATCATCACTGGCATGGTCAACCATACCGTCGa                                                            >  1:3237469/1‑41 (MQ=255)
                                      aaaCAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAg                                                  <  1:2374627/51‑1 (MQ=255)
                                       aacaacTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGt                                           <  1:1230134/57‑1 (MQ=255)
                                        acaacTCATCATCACTGGCATGGTCAACCATACCGTCGAtt                                                          <  1:2505506/41‑1 (MQ=255)
                                        acaacTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCcgc                             >  1:2734347/1‑70 (MQ=255)
                                         caacTCATCATCACTGGCATGGTGAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGa                           >  1:24462/1‑71 (MQ=255)
                                          aacTCATCATCACTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGat                          >  1:1525008/1‑71 (MQ=255)
                                            cTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatca                        <  1:3038429/71‑1 (MQ=255)
                                                tcatcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                     <  1:917093/54‑1 (MQ=255)
                                                tcatcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatcatc                      <  1:515600/69‑1 (MQ=255)
                                                  atcaCTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCAtcttct                  >  1:3620974/1‑71 (MQ=255)
                                                  atcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCaaa                                   >  1:3875235/1‑54 (MQ=255)
                                                  atcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCAtcttct                  <  1:4135958/71‑1 (MQ=255)
                                                  atcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCAtcttct                  >  1:2873893/1‑71 (MQ=255)
                                                   tcaCTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATcttctt                 <  1:1918067/71‑1 (MQ=255)
                                                     aCTGGCATGGTCAATCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTc               >  1:1189676/1‑71 (MQ=255)
                                                       tGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCACcttctt                 <  1:596069/67‑1 (MQ=255)
                                                           aTGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCAt          <  1:2060723/70‑1 (MQ=255)
                                                            tGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCaaa                                   <  1:2418638/44‑1 (MQ=255)
                                                            tGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                     <  1:2490754/42‑1 (MQ=255)
                                                            tGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                     <  1:2972155/42‑1 (MQ=255)
                                                            tGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCcgcta                           <  1:785875/52‑3 (MQ=255)
                                                            tGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGatcat                       <  1:1732654/56‑1 (MQ=255)
                                                            tGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTc            <  1:3180360/67‑1 (MQ=255)
                                                              gTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGt       >  1:2006854/1‑70 (MQ=255)
                                                               tCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGt       <  1:3507527/69‑1 (MQ=255)
                                                               tCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTaa     <  1:4613190/71‑1 (MQ=255)
                                                               tCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTaa     <  1:2127852/71‑1 (MQ=255)
                                                                  aCCATACCGTCGATTAATGCCAGAATGCGTGATTCa                                     <  1:533091/36‑1 (MQ=255)
                                                                  aCCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTAAAAc  >  1:3095003/1‑71 (MQ=255)
                                                                   |                                                                     
ATGGCTAATGTCAGGTGGCCACGCAAATACCCACTGGCAAACAACTCATCATCACTGGCATGGTCAACCATACCGTCGATTAATGCCAGAATGCGTGATTCAAACTCCGCGATCATCTTCTTTCCTCATTGTAAAAC  >  W3110S.gb/2449500‑2449636

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