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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,014,710 C→G 20.5% A453A (GCG→GCC) ‡ fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,7100CG20.5% 118.6 / 26.3 60A453A (GCG→GCC) ‡fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base C (26/21);  new base G (3/9);  total (29/31)
Fisher's exact test for biased strand distribution p-value = 1.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

TACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATA  >  minE/1014646‑1014778
                                                                |                                                                    
tACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTg                                                                 <  1:407881/70‑1 (MQ=255)
 acacGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGc                                                                <  1:3720889/70‑1 (MQ=255)
 aCAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGc                                                                <  1:1571079/70‑1 (MQ=255)
 aCAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCCCTTGc                                                                <  1:2075309/70‑1 (MQ=255)
     gCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGtt                                                            >  1:3113426/1‑70 (MQ=255)
     gCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGt                                                             >  1:1543762/1‑69 (MQ=255)
      cATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGa                                                          <  1:3804464/71‑1 (MQ=255)
       aTCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGtt                                                            <  1:3298396/68‑1 (MQ=255)
        tCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATc                                                        >  1:2074443/1‑71 (MQ=255)
            taaCCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCAcg                                                    <  1:3545738/69‑2 (MQ=255)
              aCCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTa                                                  <  1:928210/71‑1 (MQ=255)
                ctgctgGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCtt                                                                  >  1:3947847/1‑53 (MQ=255)
                  gctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGaa                                              >  1:345416/1‑71 (MQ=255)
                   ctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGa                                               <  1:3414534/69‑1 (MQ=255)
                   ctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGa                                               <  1:3387460/69‑1 (MQ=255)
                   ctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGa                                               <  1:3302231/69‑1 (MQ=255)
                      gctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGa                                                      <  1:2970784/59‑1 (MQ=255)
                      gctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatcc                                           <  1:664677/70‑1 (MQ=255)
                      actgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtcca                                          <  1:3597046/70‑1 (MQ=255)
                       ctgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtccat                                         <  1:1565129/71‑1 (MQ=255)
                        tgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatccgtc                                        >  1:453332/1‑71 (MQ=255)
                        tgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtcc                                           <  1:1060785/68‑1 (MQ=255)
                          cGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccg                                      >  1:2532283/1‑71 (MQ=255)
                           ggTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgt                                     <  1:816599/71‑1 (MQ=255)
                               gCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatc                                            <  1:2955553/60‑1 (MQ=255)
                               accTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcctg                                 >  1:723649/2‑69 (MQ=255)
                               accTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcct                                  <  1:3140327/69‑2 (MQ=255)
                                ccTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGAc                                                     >  1:2399701/1‑50 (MQ=255)
                                ccTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCcggc                                >  1:1770302/1‑71 (MQ=255)
                                 cTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtccat                                         <  1:2601338/61‑1 (MQ=255)
                                 cTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtc                                    >  1:1039793/1‑66 (MQ=255)
                                  tttCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCctgc                                <  1:586561/69‑1 (MQ=255)
                                  tttCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCg                                                       <  1:1683401/46‑1 (MQ=255)
                                   ttCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtccatac                                       >  1:118187/1‑59 (MQ=255)
                                   ttCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGt                             >  1:308783/1‑71 (MQ=255)
                                   ttCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGt                             >  1:2013825/1‑71 (MQ=255)
                                   ttCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGt                             >  1:685522/1‑71 (MQ=255)
                                    tCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGtg                            >  1:3941772/1‑70 (MQ=255)
                                    tCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGAt                                                         >  1:3395815/1‑42 (MQ=255)
                                      gCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatcc                                           >  1:654576/1‑54 (MQ=255)
                                       ccAGCATGATCATGCTGCCGCCGTG‑GATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGtt                         <  1:852026/70‑1 (MQ=255)
                                       ccAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGa                                               <  1:1092480/49‑1 (MQ=255)
                                       ccAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGtt                         >  1:2745306/1‑71 (MQ=255)
                                       ccAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGtt                         <  1:3893653/71‑1 (MQ=255)
                                        cAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTg                        <  1:2163215/71‑1 (MQ=255)
                                        cAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTg                        <  1:2047111/71‑1 (MQ=255)
                                         aGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTg                        >  1:1354929/1‑70 (MQ=255)
                                          gCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCcggc                                >  1:62955/1‑61 (MQ=255)
                                            aTGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGc                     <  1:1716779/70‑1 (MQ=255)
                                             tGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTgg                       >  1:3926520/1‑67 (MQ=255)
                                                 cATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCaa                  >  1:643730/1‑68 (MQ=255)
                                                    aCTTCCGCCCTGCGCTTGCAGTTGATCGACATAAg                                                >  1:56472/1‑35 (MQ=255)
                                                       tCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCAGGCGGTCGTTGGGCCAAGAGAAcc           >  1:474120/1‑69 (MQ=255)
                                                        ccGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCg          >  1:960034/1‑69 (MQ=255)
                                                        ccGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCg          >  1:1328016/1‑69 (MQ=255)
                                                          gCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAgg      <  1:3066225/71‑1 (MQ=255)
                                                            ccTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAg       >  1:1075183/1‑68 (MQ=255)
                                                              tGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCcggcg                               <  1:3785807/42‑1 (MQ=255)
                                                              tGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCcggcg                               <  1:2062144/42‑1 (MQ=255)
                                                              tGCCCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCAt   >  1:463026/1‑70 (MQ=255)
                                                                cgcTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATa  <  1:1936669/69‑1 (MQ=255)
                                                                |                                                                    
TACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATA  >  minE/1014646‑1014778

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