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
A6 F1 I0 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 minE 1,014,644 T→A 44.0% K475N (AAA→AAT) ‡ fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,6440TA44.0% 23.4 / 75.2 59K475N (AAA→AAT) ‡fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base T (14/19);  new base A (12/14);  total (26/33)
Fisher's exact test for biased strand distribution p-value = 7.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTAATACTTCCCTGCGCCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGC  >  minE/1014575‑1014712
                                                                     |                                                                    
ctTAATACTTCCCTGCGCCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGttttt                                                                     >  1:4765620/1‑71 (MQ=255)
          cccTGCGCCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCa                                                             <  1:5435483/69‑1 (MQ=255)
          cccTGCGCCAATACAGCGGCCGGACCACCGATACAGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCa                                                             <  1:3040774/69‑1 (MQ=255)
            cTGCGCCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGcgt                                                            <  1:2813926/68‑3 (MQ=255)
            cTGCGCCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTcgg                                                         >  1:5648506/1‑69 (MQ=255)
            cTGCGCCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTcg                                                          >  1:5141058/1‑69 (MQ=255)
            cTGCGCCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTc                                                           <  1:227697/69‑1 (MQ=255)
            cTGCGCCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCa                                                             >  1:5498553/1‑67 (MQ=255)
            cTGCGCCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCg                                                         <  1:406601/71‑1 (MQ=255)
               cgcCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGtaa                                                      >  1:4676832/1‑69 (MQ=255)
               cgcCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGta                                                       <  1:2331422/70‑2 (MQ=255)
               cgcCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGta                                                       <  1:2271464/70‑2 (MQ=255)
               cgcCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGt                                                        <  1:2188830/69‑1 (MQ=255)
               cgcCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGt                                                        <  1:3096114/69‑1 (MQ=255)
               cgcCAGTACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGt                                                        <  1:4717182/69‑1 (MQ=255)
               cgcCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTc                                                       <  1:1776041/70‑1 (MQ=255)
                  cAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACct                                                   >  1:5625313/1‑71 (MQ=255)
                  cAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACct                                                   >  1:2937934/1‑71 (MQ=255)
                   agtACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACct                                                   >  1:3344664/3‑70 (MQ=255)
                    gtACCGCCGCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACctgc                                                 >  1:401206/2‑71 (MQ=255)
                    aTACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCAt                                                            <  1:5582778/60‑1 (MQ=255)
                     tACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATcc                                                          <  1:2153796/61‑1 (MQ=255)
                     tACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACctgct                                                >  1:477448/1‑71 (MQ=255)
                      aCAGCGGCCGGACCACCGATACTGACAAGGTAGAAGCCGCCGTGTTTTTTAc                                                                  >  1:2034702/1‑52 (MQ=255)
                         gccgCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTgctgact                                            >  1:2804282/4‑71 (MQ=255)
                          ccgCCGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTgctgactg                                           >  1:1923016/3‑71 (MQ=255)
                           ggCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTAc                                                                  <  1:3324028/47‑1 (MQ=255)
                             ccGGACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCgg                                        >  1:1332908/1‑71 (MQ=255)
                               ggACCGCCGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGtt                                      <  1:3406118/71‑1 (MQ=255)
                               ggACCACCGATACTGCCAAGGTAGAAGCCGCCGTGttttt                                                                     <  1:2221431/40‑1 (MQ=255)
                                  ccgccGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTAcc                                   >  1:1428085/4‑71 (MQ=255)
                                   caccGATACTGCCAAGGTAGAAGCCGCCGTGttttt                                                                     <  1:5541609/36‑1 (MQ=255)
                                    accGATACTGCCAAGGTAGAAGCCTCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGtt                                      <  1:1485907/66‑1 (MQ=255)
                                     ccGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCttt                                <  1:2124863/71‑1 (MQ=255)
                                     ccGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCa                                                      >  1:5358990/1‑49 (MQ=255)
                                      cGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACa                                                                 >  1:1968719/1‑37 (MQ=16)
                                        aTACTGCCGAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGc                             >  1:4718648/1‑71 (MQ=255)
                                         tACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCg                                         <  1:584932/58‑1 (MQ=255)
                                             gCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATcc                                                          >  1:1468642/1‑37 (MQ=255)
                                             gCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCAc                                                     >  1:1089860/1‑42 (MQ=255)
                                              ccgaGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCAt                       >  1:4711726/4‑71 (MQ=255)
                                               cAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGt                                       >  1:3420216/1‑54 (MQ=255)
                                               cAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATg                      <  1:3314451/71‑1 (MQ=255)
                                                aaGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGa                     <  1:4642660/71‑1 (MQ=255)
                                                   gTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGc                             >  1:9102/1‑60 (MQ=255)
                                                   gTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCa                  <  1:2046162/71‑1 (MQ=255)
                                                    tAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGt                                       <  1:836799/49‑1 (MQ=255)
                                                    tAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGt                                       <  1:3664711/49‑1 (MQ=255)
                                                    tAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCa                  >  1:2626776/1‑70 (MQ=255)
                                                    tAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                 <  1:887462/71‑1 (MQ=255)
                                                    tAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAt                 <  1:2955299/71‑1 (MQ=255)
                                                     aGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                 >  1:2383907/1‑70 (MQ=255)
                                                     aGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtg                >  1:875607/1‑70 (MQ=255)
                                                      gAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtg                <  1:2329419/70‑2 (MQ=255)
                                                       aaGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtgc               <  1:3357362/70‑3 (MQ=255)
                                                       aaGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtg                <  1:3328683/69‑2 (MQ=255)
                                                       aaGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCATGCt              <  1:530231/71‑1 (MQ=255)
                                                           cgccgTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg          <  1:5149872/71‑1 (MQ=255)
                                                           cgccgTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg          <  1:4932291/71‑1 (MQ=255)
                                                           cgccgTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg          >  1:4858543/1‑71 (MQ=255)
                                                                tgtTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                 <  1:4868250/59‑1 (MQ=255)
                                                                tgtTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                 <  1:4861554/59‑1 (MQ=255)
                                                                  ttttttACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                 <  1:4304837/57‑1 (MQ=255)
                                                                   tttttACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTgcgc  >  1:3348219/1‑71 (MQ=255)
                                                                    ttttACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTc                               <  1:328727/41‑1 (MQ=255)
                                                                     |                                                                    
CTTAATACTTCCCTGCGCCAATACAGCGGCCGGACCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGC  >  minE/1014575‑1014712

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