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 2,394,072 A→G 9.2% D97G (GAT→GGT)  yfbP → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,394,0720AG 9.2% 139.4 / 6.7 54D97G (GAT→GGT) yfbPhypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (22/27);  new base G (2/3);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

AAGAAGTTCGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACGGGAAGGCTTGATGACG  >  W3110S.gb/2394005‑2394140
                                                                   |                                                                    
aagaagTTCGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATc                                                                    >  1:1281151/1‑70 (MQ=255)
  gaagTTCGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATc                                                                    >  1:703977/1‑68 (MQ=255)
      ttCGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACtt                                                             <  1:3450027/71‑1 (MQ=255)
       tCGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACttt                                                            >  1:1365290/1‑71 (MQ=255)
        cGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGAt                                                                     >  1:336422/1‑61 (MQ=255)
        cGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGAt                                                                     >  1:3798481/1‑61 (MQ=255)
        cGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTg                                                           >  1:2344375/1‑71 (MQ=255)
         gaagaaTGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGGTCAAGACTTTgc                                                          <  1:1578429/71‑1 (MQ=255)
           agaaTGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTgcag                                                        >  1:4572798/1‑71 (MQ=255)
            gaaTGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTgcagc                                                       <  1:553660/71‑1 (MQ=255)
              aTGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCaa                                                     <  1:1851223/71‑1 (MQ=255)
              aTGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCaa                                                     <  1:2143511/71‑1 (MQ=255)
                 gCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAAt                                                   <  1:1470665/70‑1 (MQ=255)
                       aGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTcc                                            >  1:1541206/1‑71 (MQ=255)
                        gTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAAtc                                                  <  1:3780568/64‑1 (MQ=255)
                        gTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCg                                           <  1:2692258/71‑1 (MQ=255)
                           aaTGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGGTCAAGACTTTGCAGCaa                                                     <  1:4455085/58‑1 (MQ=255)
                           aaTGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCgtgt                                        <  1:3386429/71‑1 (MQ=255)
                             tgatgatgaTCCCTATGAAAATGGCATCAGCATCGAAGATCAAGACt                                                              <  1:1564374/47‑1 (MQ=255)
                             tgatgatgaTCCCCATGAAAATGGCATCAGCATCGAAGGTCAAGACTTTGCAGCAAAt                                                   >  1:1470777/1‑58 (MQ=255)
                             tgatgatgaTCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTg                                      <  1:1426457/71‑1 (MQ=255)
                              gatgatgatCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTgcagca                                                      <  1:252173/54‑1 (MQ=255)
                              catgatgatCCCCATGAAAATGGCATCAGCATCGAAGa                                                                      >  1:660099/2‑38 (MQ=255)
                               atgatgatCCCCATGAAAATGGCATCAGCATCGAAGATCAAGa                                                                >  1:609985/1‑43 (MQ=255)
                                  atgatCCCCATGAAAATGGCATCAGCATCGAAGATCAAGa                                                                >  1:23974/1‑40 (MQ=255)
                                  atgatCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACtt                                                             <  1:4415558/43‑1 (MQ=255)
                                   tgatCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGa                                <  1:3145247/71‑1 (MQ=255)
                                     atCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCaaa                                                    >  1:2289000/1‑49 (MQ=255)
                                        cccATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCaa                                                     <  1:2284133/45‑1 (MQ=255)
                                          cATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCt                         >  1:2932687/1‑71 (MQ=255)
                                           aTGAAAATGGCATCAGCATCGAAGGTCAAGACTTTg                                                           <  1:4290561/36‑1 (MQ=255)
                                           aTGAAAATGGCATCAGCATCGAAGATCAAGACTTTgcagca                                                      <  1:1823155/41‑1 (MQ=255)
                                            tGAAAATGGCATCAGCATCGAAGGTCAAGACTTTGCAGCAAATCTCTTCCGTGtt                                       >  1:1790554/1‑55 (MQ=255)
                                            tGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATctct                                               >  1:2498518/1‑47 (MQ=255)
                                            tGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTg                                      <  1:1755400/56‑1 (MQ=255)
                                            tGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTc                          <  1:4630225/68‑1 (MQ=255)
                                            tGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCttt                       <  1:793642/71‑1 (MQ=255)
                                             gAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCttt                       >  1:1350517/1‑70 (MQ=255)
                                             gAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCttt                       >  1:1987635/1‑70 (MQ=255)
                                              aaaaTGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCtt                        >  1:1576829/1‑68 (MQ=255)
                                              aaaaTGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTc                      >  1:1405621/1‑70 (MQ=255)
                                              aaaaTGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTc                      >  1:1429853/1‑70 (MQ=255)
                                              aaaaTGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTc                      >  1:385402/1‑70 (MQ=255)
                                               aaaTGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCaa                    <  1:983103/71‑1 (MQ=255)
                                                 aTGGCATCAGCATCGAAGATCAAGACTTTGCAGCaa                                                     >  1:2403417/1‑36 (MQ=255)
                                                  tGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACgg                 >  1:1871490/1‑71 (MQ=255)
                                                   ggCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGa                                <  1:1734665/55‑1 (MQ=255)
                                                     cATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACggg                >  1:1131772/1‑69 (MQ=255)
                                                        cAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAAc                   <  1:2547788/63‑1 (MQ=255)
                                                          gCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACGGGAAGGCtt         <  1:4488526/71‑1 (MQ=255)
                                                             tCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGATATGTCTTTCAACGGGAAGGCTtgat      <  1:4591363/71‑1 (MQ=255)
                                                              cGAAGATCAAGACTTTGCAGCAAATCTCTTCCgtt                                         <  1:4266905/35‑2 (MQ=255)
                                                               gAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACGGGAAGGCTtgatga    <  1:2247161/71‑1 (MQ=255)
                                                               gAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACGGGAAGGCTtgatg     <  1:2157851/70‑1 (MQ=255)
                                                                 aGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACGGGAAGGCTTGATGACg  <  1:930679/71‑1 (MQ=255)
                                                                   aTCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGa                                <  1:4573157/39‑1 (MQ=255)
                                                                   aTCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGa                                <  1:2814383/39‑1 (MQ=255)
                                                                   aTCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGa                                <  1:2549285/39‑1 (MQ=255)
                                                                   aTCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCtt                        <  1:2010360/47‑1 (MQ=255)
                                                                   aTCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTAGGAAATGTCt                         <  1:1862718/46‑1 (MQ=255)
                                                                   |                                                                    
AAGAAGTTCGAAGAATGGCTGGAAGTGAATGATGATGATCCCCATGAAAATGGCATCAGCATCGAAGATCAAGACTTTGCAGCAAATCTCTTCCGTGTTGCTCGGAAATGTCTTTCAACGGGAAGGCTTGATGACG  >  W3110S.gb/2394005‑2394140

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