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 609,204 A→C 22.5% V350V (GTT→GTG)  pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported609,2040AC22.5% 132.0 / 49.3 80V350V (GTT→GTG) pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base A (34/28);  new base C (13/5);  total (47/33)
Fisher's exact test for biased strand distribution p-value = 2.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGTTCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGCCAGAGA  >  Exported/609139‑609271
                                                                 |                                                                   
aTGTTCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTa                                                                     >  1:3061706/1‑66 (MQ=255)
aTGTTCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAg                                                                >  1:1055736/1‑71 (MQ=255)
  gTTCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAggg                                                              >  1:1284140/1‑71 (MQ=255)
   ttCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTaa                                                                    >  1:260483/1‑64 (MQ=255)
   ttCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAggg                                                              >  1:675934/1‑70 (MQ=255)
    tCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTa                                                            >  1:251769/1‑71 (MQ=255)
    tCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTa                                                            >  1:359129/1‑71 (MQ=255)
     cGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTAc                                                           >  1:5628799/1‑71 (MQ=255)
          ccGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCg                                                      >  1:3917869/1‑71 (MQ=255)
           cGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCg                                                      <  1:4329675/70‑1 (MQ=255)
            ggAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTc                                                    <  1:5267283/71‑1 (MQ=255)
            ggAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTc                                                    <  1:4430501/71‑1 (MQ=255)
               gaCGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAg                                                 <  1:1688737/71‑1 (MQ=255)
                  ggccccATAGTGTGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGccc                                              >  1:88760/4‑71 (MQ=255)
                  ggACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAgg                                                               >  1:3280802/1‑54 (MQ=255)
                  ggACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGcc                                              >  1:4277363/1‑71 (MQ=255)
                  ggACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGcc                                              <  1:4683451/71‑1 (MQ=255)
                  ggACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGcc                                              <  1:831753/71‑1 (MQ=255)
                   gccccATAGTGTGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGccc                                              >  1:5585024/3‑70 (MQ=255)
                   gccccATAGTGTGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGccc                                              >  1:1969608/3‑70 (MQ=255)
                     cccATAGTGTGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCAt                                           >  1:2876034/1‑71 (MQ=255)
                      ccATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGa                                                  >  1:3538263/1‑63 (MQ=255)
                      ccATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGa                                                  >  1:1727957/1‑63 (MQ=255)
                       cATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATac                                         <  1:1498445/71‑1 (MQ=255)
                       cATAGTGTGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCAtcc                                         <  1:28585/71‑3 (MQ=255)
                        aTGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATac                                         >  1:3725049/1‑70 (MQ=255)
                         tGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATacca                                       >  1:1355781/1‑71 (MQ=255)
                           gtgtGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATcccgcc                                     >  1:3131886/1‑71 (MQ=255)
                           gtgtGCAGGGTGTGCAAATAGCGGAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATcccgc                                      >  1:4181715/1‑68 (MQ=255)
                           gtgtACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATaccac                                      >  1:1664215/1‑70 (MQ=255)
                              tACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAAcc                                                                  <  1:5088391/39‑1 (MQ=255)
                              tACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAAcc                                                                  <  1:3399252/39‑1 (MQ=255)
                              tACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAAcc                                                                  <  1:3078938/39‑1 (MQ=255)
                              tACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGAt                                  <  1:2213120/71‑1 (MQ=255)
                                cAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGa                                   >  1:1558318/1‑68 (MQ=255)
                                cAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATa                                 <  1:4373535/70‑1 (MQ=255)
                                  gggTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATAACACCGATAGAt                              <  1:4219930/71‑1 (MQ=255)
                                       ttCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGcc                                              <  1:2075826/50‑1 (MQ=255)
                                       ttCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGcc                                              <  1:1232033/50‑1 (MQ=255)
                                       ttCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGt                         >  1:146097/1‑71 (MQ=255)
                                         cAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATac                                         >  1:1681998/1‑53 (MQ=255)
                                          aGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTg                       <  1:1815458/70‑1 (MQ=255)
                                          aGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGc                      <  1:3223435/71‑1 (MQ=255)
                                              aaCGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCAt                                           >  1:180679/1‑46 (MQ=255)
                                              aaCGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAg                  <  1:5120824/71‑1 (MQ=255)
                                               aCGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGa                 <  1:1618778/71‑1 (MQ=255)
                                                cGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCg                                    >  1:254371/1‑51 (MQ=255)
                                                cGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGa                                   >  1:3229867/1‑52 (MQ=255)
                                                cGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGa                                   >  1:1655566/1‑52 (MQ=255)
                                                cGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGcc                     >  1:2858751/1‑66 (MQ=255)
                                                cGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGAt                <  1:1468218/71‑1 (MQ=255)
                                                 ggAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAt                                  >  1:2928662/1‑52 (MQ=16)
                                                 ggAAGGAGTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAt                                  >  1:3848782/1‑52 (MQ=16)
                                                 ggAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCAt                                           >  1:3627170/1‑43 (MQ=255)
                                                 ggAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATa                                          >  1:2470007/1‑44 (MQ=255)
                                                 ggAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGcc                     >  1:4980736/1‑65 (MQ=255)
                                                    aGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCgg             <  1:2476638/70‑1 (MQ=255)
                                                     ggagTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGATCACTTCCGTCGCCCAGATTGGGt           <  1:2964678/68‑1 (MQ=255)
                                                        gTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAtca                                >  1:1750265/1‑45 (MQ=16)
                                                        gTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAtca                                >  1:417144/1‑45 (MQ=16)
                                                        gTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAtca                                >  1:5579429/1‑45 (MQ=16)
                                                        gTTTTTGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAtca                                >  1:2007762/1‑45 (MQ=16)
                                                        gTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCgg                          >  1:4654558/1‑53 (MQ=255)
                                                         tttttGGTCACCAGCGTACGACCGTCCAGCCCCATcccgc                                      <  1:2577542/40‑3 (MQ=12)
                                                         tttttGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGAtc                                 <  1:3875433/45‑2 (MQ=12)
                                                         tttttGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGATCACTTCCGTCGCCCAGATTggg            >  1:4588029/1‑66 (MQ=255)
                                                         tttttGGTAACCAGGGTACGACCGTCGAGGCCCATa                                          <  1:1174576/36‑1 (MQ=255)
                                                         tttttGGTAACCAGGGTACGACCGTCGAGGCCCATa                                          <  1:1202690/36‑1 (MQ=255)
                                                         tttttGGTAACCAGGGTACGACCGTCGAGGCCCATa                                          <  1:3431981/36‑1 (MQ=255)
                                                         tttttGGTAACCAGGGTACGACCGTCGAGGCCCATa                                          <  1:3161205/36‑1 (MQ=255)
                                                         tttttGGTAACCAGGGTACGACCGTCGAGGCCCATa                                          <  1:1735616/36‑1 (MQ=255)
                                                         tttttGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGc        <  1:151642/70‑1 (MQ=255)
                                                          ttttGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGc        >  1:1515688/1‑69 (MQ=255)
                                                          ttttGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGc        >  1:2138134/1‑69 (MQ=255)
                                                           tttGGTAACCAGGGTACGACCGTCGAGGCCCATacca                                       >  1:1993855/1‑37 (MQ=255)
                                                           tttGGTAACCAGGGTACGACCGTCGAGGCCCATacc                                        >  1:266622/1‑36 (MQ=255)
                                                           tttGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCg              >  1:2000489/1‑62 (MQ=255)
                                                           tttGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGcc       >  1:2712682/1‑69 (MQ=255)
                                                           tttGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGcc       >  1:2474570/1‑69 (MQ=255)
                                                            ttGGTCACCAGCGTACGACCGTCCAGCCCCATCCCGCCGATCACTTCCGTCGCCCAGATTGGGTCGccgg     <  1:1269378/70‑3 (MQ=255)
                                                              ggTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGCCagag   >  1:1969865/1‑70 (MQ=255)
                                                               gTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGCCAgaga  <  1:2512797/70‑1 (MQ=255)
                                                                 |                                                                   
ATGTTCGGTTCCGGAGACGGACCCATGGTGTACAGGGTGTTCAGGAAACGGAAGCTGTTTTTGGTAACCAGGGTACGACCGTCGAGGCCCATACCACCGATAGATTCGGTTGCCCAGATCGGGTCGCCAGAGA  >  Exported/609139‑609271

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