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 609,794 T→A 25.5% T154S (ACT→TCT) ‡ pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported609,7940TA25.5% 197.3 / 72.2 106T154S (ACT→TCT) ‡pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base T (42/37);  new base A (14/13);  total (56/50)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.88e-01

Only 100 of 106 total aligned reads displayed.

CCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGATTTTTTTG  >  Exported/609727‑609852
                                                                   |                                                          
ccacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGTCAACGCAGGATGTCCGGAGTGTa                                                         <  1:4426013/71‑1 (MQ=255)
ccacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa                                                         <  1:119365/71‑1 (MQ=255)
ccacggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa                                                         <  1:4890959/71‑1 (MQ=255)
 cacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaa                                                        <  1:609488/71‑1 (MQ=255)
 cacggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa                                                         <  1:472761/70‑1 (MQ=255)
 cacggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTaa                                                        <  1:5234997/71‑1 (MQ=255)
  acggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTaaa                                                       >  1:1256356/1‑71 (MQ=255)
  acggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa                                                         <  1:826443/69‑1 (MQ=255)
   cggccaTATGCATCTGGCAGACCTTTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaaa                                                       >  1:2340349/1‑70 (MQ=255)
   cggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaaa                                                       >  1:1699264/1‑70 (MQ=255)
   cggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAAc                                                      >  1:5312540/1‑71 (MQ=255)
   cggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAAc                                                      >  1:2896784/1‑71 (MQ=255)
    ggccaTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACg                                                     <  1:114108/71‑1 (MQ=255)
    ggccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAAca                                                     <  1:5066423/71‑2 (MQ=255)
      ccaTAGCCATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATc                                                   <  1:4805222/71‑1 (MQ=255)
       caTATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCg                                                  <  1:1392433/71‑1 (MQ=255)
         tatGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa                                                         <  1:2781513/62‑1 (MQ=255)
         tatGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                <  1:1112119/71‑1 (MQ=255)
         tatGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                <  1:4442888/71‑1 (MQ=255)
          agccATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCaaa                                                >  1:4424970/4‑70 (MQ=255)
          agccATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCaaa                                                >  1:4223194/4‑70 (MQ=255)
          agccATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCaaa                                                >  1:2467907/4‑70 (MQ=255)
           tGCATCTGGCAGACCGGGCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAaca                                              >  1:3822322/1‑71 (MQ=255)
           gccATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTaaa                                                       >  1:35780/3‑62 (MQ=255)
           gccATCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCaaat                                               <  1:4228793/68‑2 (MQ=255)
               tCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa                                                         <  1:685436/56‑1 (MQ=255)
               tCTGGTAAACCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTa                                                         <  1:145809/56‑1 (MQ=255)
               tCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa                                                         <  1:5121823/56‑1 (MQ=255)
                cTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGccc                                         >  1:4247352/1‑71 (MQ=255)
                 tGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa                                                         <  1:1846544/54‑1 (MQ=255)
                 tGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCg                                                  >  1:3039087/1‑61 (MQ=255)
                 tGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCt                                        >  1:5075076/1‑71 (MQ=255)
                    cAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                >  1:1376146/1‑60 (MQ=255)
                    cAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                >  1:3868989/1‑60 (MQ=255)
                    cAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                >  1:4702682/1‑60 (MQ=255)
                    cAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGT‑CGGAGTGTAAACGTCGaa                                                >  1:4552518/1‑59 (MQ=255)
                     aaaCCGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGt                                     >  1:1024750/3‑70 (MQ=255)
                       aCCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTtgt                                  <  1:183171/71‑1 (MQ=255)
                         cGGTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGTtatgg                                >  1:3710304/1‑70 (MQ=255)
                          ggTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTa                                                         <  1:3069347/45‑1 (MQ=255)
                           gTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGccc                                         >  1:5571530/1‑60 (MQ=12)
                           gTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGccc                                         >  1:4581481/1‑60 (MQ=12)
                           gTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGccc                                         >  1:4575174/1‑60 (MQ=12)
                           gTCAGCACGCCAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGccc                                         >  1:4106300/1‑60 (MQ=12)
                           gTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAaca                                              >  1:1149188/1‑55 (MQ=255)
                           gTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAac                                               >  1:1333273/1‑54 (MQ=255)
                            tCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaaa                                                       >  1:2025101/1‑45 (MQ=255)
                            tCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTaaa                                                       >  1:3094220/1‑45 (MQ=255)
                             cAGAACACCAGATTTACGGCAACGCATGATGTCCGGAGTGTAAACGTCg                                                  <  1:417847/49‑1 (MQ=255)
                              aGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGttt                            >  1:4540961/1‑70 (MQ=255)
                               gAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTTAACGTCGaa                                                >  1:4909086/1‑49 (MQ=255)
                               gAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                >  1:2810451/1‑49 (MQ=255)
                               gAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                >  1:1354427/1‑49 (MQ=255)
                                aaCACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAaca                                              >  1:3661589/1‑50 (MQ=255)
                                aaCACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTa                          >  1:1366394/1‑70 (MQ=255)
                                    ccAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGTTATGGGTTTTACgcag                     <  1:5526446/71‑4 (MQ=255)
                                     cAGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGTTATGGGTTTTACg                        >  1:4448415/1‑67 (MQ=255)
                                      aGATTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGTTATGGGTTTTACg                        >  1:5020873/1‑66 (MQ=255)
                                      aGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTAtt                   >  1:4220959/1‑71 (MQ=255)
                                       gATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAaca                                              >  1:425310/1‑43 (MQ=255)
                                       gATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTAtt                   >  1:5335648/1‑70 (MQ=255)
                                       gATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTc                  <  1:2987674/71‑1 (MQ=255)
                                        aTTTACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGTTATGGGt                              <  1:1816085/58‑1 (MQ=12)
                                         tttACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGa                                                 >  1:5605969/1‑38 (MQ=255)
                                         tttAAGGCAACGCAGGATGTCCGGAGTGTAAACGTCGaa                                                >  1:5282951/1‑39 (MQ=255)
                                           tACGGCAGCGCAGCATATCCGGTGAGTAAACATCAAATACGCCCTGGTTATGGGTTTTACg                        >  1:624521/1‑61 (MQ=16)
                                           tACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGa                                <  1:718323/53‑1 (MQ=255)
                                           tACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGa                                <  1:5670167/53‑1 (MQ=255)
                                            aCGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTg              >  1:4481659/1‑70 (MQ=255)
                                               gCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGa                                <  1:257130/49‑1 (MQ=255)
                                                cAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGtttt                           >  1:1238475/1‑53 (MQ=255)
                                                 aaCGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAtt        >  1:3581036/1‑71 (MQ=255)
                                                  aCGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTg              >  1:2324190/1‑64 (MQ=255)
                                                  aCGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTg              <  1:2607159/64‑1 (MQ=255)
                                                   cGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAtttt      <  1:1350574/71‑1 (MQ=255)
                                                    gCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTa                          >  1:1039979/1‑50 (MQ=255)
                                                    gCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTa                          >  1:708863/1‑50 (MQ=255)
                                                    gCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAttttt     <  1:1592137/71‑1 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACg                        >  1:683568/1‑51 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACg                        >  1:2670501/1‑51 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACg                        >  1:3635746/1‑51 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACg                        >  1:1739280/1‑51 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACg                        >  1:2460056/1‑51 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAtttttt    >  1:2801026/1‑71 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAtttttt    >  1:1047864/1‑71 (MQ=255)
                                                     cAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAttttt     <  1:5433830/70‑1 (MQ=255)
                                                       ggATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAg                               <  1:3102581/42‑1 (MQ=255)
                                                       ggATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCGGTGAAGATTTTTTTg  <  1:1513943/71‑1 (MQ=255)
                                                       ggATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGATTTTTTTg  <  1:3189165/71‑1 (MQ=255)
                                                        gATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTa                          <  1:3490918/46‑1 (MQ=255)
                                                           gTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGt                              <  1:166337/39‑1 (MQ=255)
                                                           gTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGt                              <  1:3298447/39‑1 (MQ=255)
                                                           gTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGt                              <  1:2950033/39‑1 (MQ=255)
                                                           gTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGt                              <  1:1694819/39‑1 (MQ=255)
                                                             ccGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAttttt     <  1:4760888/62‑1 (MQ=255)
                                                              cGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGttt                            <  1:1222441/38‑1 (MQ=255)
                                                              cGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTc                  <  1:4623315/48‑1 (MQ=255)
                                                              cGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAttttt     <  1:1991010/61‑1 (MQ=255)
                                                                gAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAttttttt   <  1:2310444/61‑1 (MQ=255)
                                                                 aGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGAttttttt   <  1:210451/60‑1 (MQ=255)
                                                                   |                                                          
CCACGGCCATATGCATCTGGCAGACCGGTCAGAACACCAGATTTACGGCAACGCAGGATGTCCGGAGTGTAAACGTCGAACACGCCCTGGTTGTGAGTTTTACGGTATTCAGTGAAGATTTTTTTG  >  Exported/609727‑609852

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