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 223,018 C→A 25.3% intergenic (+73/‑107) lpcA → / → prfH D‑sedoheptulose 7‑phosphate isomerase/predicted peptide chain release factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported223,0180CA25.3% 159.9 / 64.2 122intergenic (+73/‑107)lpcA/prfHD‑sedoheptulose 7‑phosphate isomerase/predicted peptide chain release factor
Reads supporting (aligned to +/- strand):  ref base C (49/42);  new base A (10/21);  total (59/63)
Fisher's exact test for biased strand distribution p-value = 6.01e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 123 total aligned reads displayed.

CTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCACGCCGCATCCGA  >  Exported/222948‑223086
                                                                      |                                                                    
cTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGAc                                                                      >  1:434380/1‑71 (MQ=255)
    tgTAGGCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCt                                                                <  1:3991590/70‑1 (MQ=9)
    tgTAGGCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCt                                                                <  1:4325091/70‑1 (MQ=9)
        ggCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTa                                                              <  1:3968490/71‑1 (MQ=255)
        ggCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTa                                                              >  1:4039942/1‑71 (MQ=255)
        ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt                                                             >  1:2766014/1‑70 (MQ=9)
        ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt                                                             <  1:3118110/70‑1 (MQ=9)
        ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt                                                             <  1:4582333/70‑1 (MQ=9)
        ggCCGGACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt                                                             <  1:4683535/70‑1 (MQ=9)
        ggCCGGACAAGACGTTTA‑‑TCGAATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTAt                                                             <  1:834604/70‑1 (MQ=2)
         gCCGGATAAGGCGTTTATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTa                                                              >  1:4619478/1‑70 (MQ=11)
           cGGATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGt                                                                  <  1:2226868/64‑1 (MQ=14)
            ggATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTAt                                                             >  1:1063915/1‑68 (MQ=14)
            ggACAAGACGTTTA‑‑TCGCATCCGGCAGTCGTGTGCAGATGCCTGATGCGACGCTAACGCGTCTTATc                                                            <  1:3573976/67‑1 (MQ=9)
             gATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCagg                                                         >  1:4350560/1‑69 (MQ=11)
             gATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCagg                                                         >  1:824945/1‑69 (MQ=11)
             gATAAGGCGTTTACGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCagg                                                         >  1:5554197/1‑69 (MQ=11)
               tAAGGCGTTTACGCCGCATCCGGCAGTTGTACGCAGGTGCCTGATGCGACGCTGGCGCGTCTTATCATGcc                                                       <  1:3814930/71‑1 (MQ=11)
                 aggcGTTTATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTa                                                     <  1:1875605/68‑1 (MQ=11)
                 aggcGTTTACGCCGCATCCGGCAGTTGTACGCAGGTGCCTGATGCGACGCTGGCGCGTCTTATCATGCCt                                                      <  1:75157/67‑1 (MQ=11)
                 aGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTa                                                     >  1:3666333/1‑71 (MQ=255)
                  ggcGTTTACGCCGCATCCGGCAGTTGTACGCAGGTGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTAc                                                    <  1:5436686/69‑1 (MQ=11)
                     gTTTATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACaaa                                                 >  1:1943052/1‑71 (MQ=14)
                     gTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATg                                                         >  1:1076548/1‑63 (MQ=255)
                     gTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACaaa                                                 >  1:2742367/1‑71 (MQ=255)
                      tttATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATc                                                            <  1:3095830/59‑1 (MQ=11)
                      ttcaCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGACCTACAAAt                                                <  1:316021/68‑1 (MQ=11)
                       ttATGCCGCATCCGGCAGTTATGCGCAGATGCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACaaact                                               >  1:187324/1‑69 (MQ=11)
                       ttACGCCGCATCCGGCATTTGTGCGATGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATc                                               >  1:2157744/1‑71 (MQ=255)
                        tACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCt                                              >  1:5551855/1‑71 (MQ=255)
                        caCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAtt                                               >  1:3545990/2‑69 (MQ=11)
                        caCGCCGCATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGACCTACAAAttc                                              >  1:2380082/2‑69 (MQ=11)
                            ccgcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAc                                          <  1:5228399/71‑1 (MQ=255)
                             cgcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAcg                                         <  1:4007667/71‑1 (MQ=255)
                             cgcATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGt                                                                  >  1:557805/1‑46 (MQ=14)
                              gcATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAcgc                                        >  1:3970778/1‑71 (MQ=255)
                              gcATCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACa                                                   <  1:1360600/60‑1 (MQ=11)
                               cATCCGGCA‑CTGTGTGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGCCTAcg                                                   <  1:1850183/58‑2 (MQ=14)
                                 tCCGGCAGTCGTGCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAttc                                              >  1:1944324/1‑60 (MQ=11)
                                      cATTTGTGCGCTGATGCCTGATGCGACGCTGCCGCGTCTTATCATGCCTACAAATCTGTACGCGAACCg                                  >  1:1816658/1‑69 (MQ=255)
                                      cATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTa                                <  1:1381827/71‑1 (MQ=255)
                                        tttGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACaa                                                  <  1:1505484/51‑1 (MQ=255)
                                         ctgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTATCAt                                                          <  1:1633189/41‑1 (MQ=14)
                                         ctgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTATCAt                                                          <  1:3307470/41‑1 (MQ=14)
                                          tgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTAt                                                             <  1:599282/38‑1 (MQ=14)
                                          tgtgtgCCGATGCCTGATGCGACGCTGACGCGTTTTAt                                                             <  1:4718543/38‑1 (MQ=14)
                                          tgtgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAg                               >  1:2547384/1‑68 (MQ=255)
                                          tgtgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAg                               >  1:3118635/1‑68 (MQ=255)
                                          tgtgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGcc                            >  1:2958194/1‑71 (MQ=255)
                                           gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc                                                        >  1:1661702/1‑42 (MQ=14)
                                           gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc                                                        >  1:2721273/1‑42 (MQ=14)
                                           gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGc                                                        >  1:4043461/1‑42 (MQ=14)
                                           gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGCCTa                                                     >  1:3473134/1‑45 (MQ=11)
                                           gtgtGCCGATGCCTGATGCGACGCTGACGCGTTTTATCATGCCTa                                                     >  1:3616852/1‑45 (MQ=11)
                                           gtgCGCAGATGCCTGATGCGACGCTAACGCGTCTTATCAGGCCTACAAAtt                                               >  1:4971846/1‑50 (MQ=14)
                                            tgCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGa                          <  1:2791128/71‑1 (MQ=255)
                                              cgcTGATGCCTGATGTGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaa                         <  1:2414668/70‑1 (MQ=255)
                                              cgcTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGcc                            <  1:1277350/67‑1 (MQ=255)
                                               gcTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaata                       <  1:14595/71‑1 (MQ=255)
                                                cctatgcctgatgcgacGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtt                                <  1:1427658‑M1/58‑20 (MQ=255)
                                                 tgatgcctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGaataat                     >  1:3498067/1‑71 (MQ=255)
                                                 ctatgcctgatgcgaCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatc                     <  1:4228679‑M1/69‑31 (MQ=255)
                                                 ctatgcctgatgcgaCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatc                     <  1:1437379‑M1/69‑31 (MQ=255)
                                                 ctatgcctgatgcgaCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgttta                              >  1:875263‑M1/3‑41 (MQ=255)
                                                  tatgcctgatgcgACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatcc                    >  1:1004805‑M1/2‑40 (MQ=255)
                                                  tatgcctgatgcgACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatcc                    >  1:2101907‑M1/2‑40 (MQ=255)
                                                  tatgcctgatgcgACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatcc                    >  1:1903227‑M1/2‑40 (MQ=255)
                                                  gatgcctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATg                    >  1:1984470/1‑71 (MQ=255)
                                                   atgcctgatgcGACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatc                     >  1:2946535‑M1/1‑39 (MQ=255)
                                                     gcctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTCTACGCGAACCGTAGGc                             >  1:4099538/1‑59 (MQ=255)
                                                     gcctgatgcGACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtat                                   <  1:2568832‑M1/53‑17 (MQ=255)
                                                      cctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGtt                <  1:3815614/71‑1 (MQ=255)
                                                       ctgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTAcgcg                                       >  1:88171/1‑47 (MQ=255)
                                                        tgatgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGtt                <  1:2198426/69‑1 (MQ=255)
                                                        tgatgcGACGCTAACGCGTCTTATCATGCCTACAAATcgc                                             <  1:5430110/40‑3 (MQ=14)
                                                         gatgcGACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtt                                <  1:5660260‑M1/52‑20 (MQ=255)
                                                         gatgcGACGCTGAAGCGTCTTATCAAGCCTACAtagcactgccacgtatgtttacaccgcatccggcata              >  1:818729‑M1/1‑33 (MQ=255)
                                                          atgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCa              >  1:1062898/1‑69 (MQ=255)
                                                          atgcGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCAcg            >  1:3836249/1‑71 (MQ=255)
                                                          atgcGACGCTGAAGCGTCTTATCATGCCTACAtagcac                                             >  1:4033205‑M1/1‑32 (MQ=255)
                                                           tgcGACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataa             <  1:4048171‑M1/69‑39 (MQ=255)
                                                           tgcGACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataa             <  1:2484138‑M1/69‑39 (MQ=255)
                                                           tgcGACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataa             <  1:2048094‑M1/69‑39 (MQ=255)
                                                            gcGACGCTAACGCGTCTTATCAGCCCTACAAATTCTCACGCCATCCGTAGGCCGGATAAGGCGTTCAcgcc          >  1:3373977/1‑71 (MQ=9)
                                                             cGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGt                                 <  1:421325/47‑1 (MQ=255)
                                                             cGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGt                                 <  1:2338056/47‑1 (MQ=255)
                                                              gACGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataaaaaca        >  1:1857692‑M1/1‑28 (MQ=255)
                                                               aCGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGcc                            <  1:5142139/50‑1 (MQ=255)
                                                               aCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataaaaa          <  1:1281470‑M1/68‑42 (MQ=255)
                                                               aCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataaaaa          <  1:3098024‑M1/68‑42 (MQ=255)
                                                               aCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatg                                  <  1:1429198‑M1/44‑18 (MQ=255)
                                                               aCGCTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatg                                  <  1:769342‑M1/44‑18 (MQ=255)
                                                                cGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCACGCCGCAt      >  1:4647210/1‑71 (MQ=255)
                                                                 gCTGACGCGTCTTATCATGCCTACAAATCTGTAcgcg                                       >  1:4238763/1‑37 (MQ=255)
                                                                  cTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCAcgc           >  1:1281187/1‑64 (MQ=255)
                                                                  cTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataaaaacacgcg    <  1:3770558‑M1/71‑48 (MQ=255)
                                                                  cTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataaaaacacgcg    <  1:4858968‑M1/71‑48 (MQ=255)
                                                                  cTGAAGCGTCTTATCATGCCTACAtagcactgccacgtatgtttacaccgcatccggcataaa            <  1:2391419‑M1/63‑40 (MQ=255)
                                                                   tGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGcc                            <  1:1671084/46‑1 (MQ=255)
                                                                    gACGCGACTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCACGCCGCATCCGa  >  1:732620/1‑71 (MQ=255)
                                                                      |                                                                    
CTGGCGTAGGCCGGATAAGACGTTTACGCCGCATCCGGCATTTGTGCGCTGATGCCTGATGCGACGCTGACGCGTCTTATCATGCCTACAAATCTGTACGCGAACCGTAGGCCGAATAATGCGTTCACGCCGCATCCGA  >  Exported/222948‑223086

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