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 664,084 C→T 16.0% G101D (GGC→GAC)  dacA ← D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb664,0840CT16.0% 140.7 / 18.0 57G101D (GGC→GAC) dacAD‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base C (20/27);  new base T (5/4);  total (26/31)
Fisher's exact test for biased strand distribution p-value = 4.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATGCCCGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGTAACTGGTCA  >  W3110S.gb/664014‑664153
                                                                      |                                                                     
cATGCCCGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGc                                                                       >  1:4157681/1‑71 (MQ=255)
cATGCCCGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGc                                                                       >  1:1714465/1‑71 (MQ=255)
    cccGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGTCGa                                                                    >  1:2751258/1‑70 (MQ=255)
    cccGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGa                                                                    >  1:3988790/1‑70 (MQ=255)
    cccGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGAt                                                                   <  1:601572/71‑1 (MQ=255)
          ttGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGa                                                              >  1:389635/1‑70 (MQ=255)
          ttGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGa                                                              >  1:4305140/1‑70 (MQ=255)
             aGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTaa                                                          <  1:2317783/71‑1 (MQ=255)
                  cATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGTCGa                                                                    <  1:1325394/56‑1 (MQ=255)
                  cATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAg                                                     <  1:2855363/71‑1 (MQ=255)
                   aTCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGt                                                    >  1:1465259/1‑71 (MQ=255)
                    tCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTaa                                                          <  1:3956137/64‑1 (MQ=255)
                    tCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAAt                                                        <  1:822751/66‑1 (MQ=255)
                      aGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGttt                                                  <  1:1172034/70‑1 (MQ=255)
                          aagaaCCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATc                                                       <  1:815875/61‑1 (MQ=255)
                             aaCCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGAt                                                                   <  1:1120439/46‑1 (MQ=255)
                             aaCCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAAt                                          >  1:2636778/1‑71 (MQ=255)
                              aCCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAAtt                                         <  1:1055156/71‑1 (MQ=255)
                               ccTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAAttt                                        <  1:3769857/71‑1 (MQ=255)
                                cTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTa                                       <  1:2561233/71‑1 (MQ=255)
                                 tttAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTaaa                                           <  1:2068865/66‑1 (MQ=255)
                                   tAAACACCAGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGt                                                                <  1:3567698/43‑1 (MQ=255)
                                        acCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCttt                               <  1:1697162/71‑1 (MQ=255)
                                         ccGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTc                              <  1:3160079/71‑1 (MQ=255)
                                          cGGGTTACCGGTGGCCCATGCGTCGTTGTAGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCa                             <  1:4222142/71‑1 (MQ=255)
                                          cGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTc                              <  1:3891371/70‑1 (MQ=255)
                                             gTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAAttt                                        <  1:3637887/57‑1 (MQ=255)
                                              ttACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATc                                                       <  1:2661065/41‑1 (MQ=255)
                                               tACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGt                                                    >  1:4185769/1‑43 (MQ=255)
                                                 ccGGTGGCCCATGCGTCGTTGTCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTg                      >  1:4585773/1‑71 (MQ=255)
                                                   ggTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCg                                    <  1:3558651/55‑1 (MQ=255)
                                                   ggTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGc                    >  1:2057550/1‑71 (MQ=255)
                                                    gTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCttt                               <  1:1235505/59‑1 (MQ=255)
                                                    gTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCa                             >  1:1023692/1‑61 (MQ=255)
                                                     tGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGc                                  >  1:3459825/1‑55 (MQ=255)
                                                        cccATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATa               <  1:3225865/71‑1 (MQ=255)
                                                         ccATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTAc                                      <  1:1915220/47‑1 (MQ=255)
                                                          cATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAAtt                                         <  1:2543018/43‑1 (MQ=255)
                                                          cATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAAtt                                         <  1:1728124/43‑1 (MQ=255)
                                                            tGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGc                         <  1:846834/57‑1 (MQ=255)
                                                            tGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGt           <  1:1677735/71‑1 (MQ=255)
                                                             gCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGt           >  1:1093855/1‑70 (MQ=255)
                                                             gCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGt           >  1:2214707/1‑70 (MQ=255)
                                                              cgtcgtTGTCGATAGTGACTAAATCAGTTTCTTTAAATTTACCg                                    <  1:852324/44‑1 (MQ=255)
                                                              cgtcgtTGTCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGTa          <  1:416168/70‑1 (MQ=255)
                                                              cgtcgtTGCCGATAGTGACTAAATCAGTTTCTTTaa                                            >  1:2103436/1‑36 (MQ=255)
                                                              cgtcgtTGCCGATAGTGACTAAATCAGTTTCTTTAAAt                                          >  1:4143548/1‑38 (MQ=255)
                                                              cgtcgtTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCa                             >  1:4038601/1‑51 (MQ=255)
                                                              cgtcgtTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCt                       >  1:1196154/1‑57 (MQ=255)
                                                              cgtcgtTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGTaa         >  1:3286823/1‑71 (MQ=255)
                                                              cgtcgtTGCCGATAGTGACTAAATAAGTTTCTTTAAAt                                          >  1:3524128/1‑38 (MQ=255)
                                                              cgtcgtTGCCGATAGTGAATAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGTaa         >  1:4507112/1‑71 (MQ=255)
                                                               gtcgtTGTCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCAt                            >  1:3611793/1‑51 (MQ=255)
                                                               gtcgtTGTCCATAGTGACTAAATCAGATTCTTTAAATTTAccc                                    >  1:2053453/1‑42 (MQ=37)
                                                                tcgtTGTCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGc                                  >  1:1813856/1‑44 (MQ=255)
                                                                  gtTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCa                             >  1:160499/1‑47 (MQ=255)
                                                                  gtTGACGATAGTGACTAAATCAGTTTCTTTAAAttt                                        >  1:211919/1‑36 (MQ=255)
                                                                   ttGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCttt                               <  1:1005844/44‑1 (MQ=255)
                                                                     gCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGTAACTGGtca  >  1:3235725/1‑71 (MQ=255)
                                                                      |                                                                     
CATGCCCGGTTTGAGGAACATCAGCGAAGAACCTTTAAACACCGGGTTACCGGTGGCCCATGCGTCGTTGCCGATAGTGACTAAATCAGTTTCTTTAAATTTACCGGCTTTCATTGCCTGGCCGATAACGTAACTGGTCA  >  W3110S.gb/664014‑664153

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