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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,968,090 T→C 28.3% A180A (GCA→GCG)  tktA ← transketolase 1, thiamin‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,968,0900TC28.3% 96.5 / 40.7 95A180A (GCA→GCG) tktAtransketolase 1, thiamin‑binding
Reads supporting (aligned to +/- strand):  ref base T (13/55);  new base C (19/8);  total (32/63)
Fisher's exact test for biased strand distribution p-value = 5.15e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGCGGTGTCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTCCAT  >  minE/1968024‑1968155
                                                                  |                                                                 
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:1052521/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:3144308/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:3086030/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:3080046/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2935117/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2786112/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:323185/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2683537/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2657359/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:368344/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2522011/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2368855/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2338569/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:514886/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:2213777/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:1670750/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:1211944/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:1117582/1‑69 (MQ=255)
tGCGGTGTCGTCGGTAAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGc                                                                 >  1:1532532/1‑69 (MQ=255)
    gtgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAAt                                                              <  1:1252853/68‑1 (MQ=255)
    gtgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAAt                                                              <  1:2562002/68‑1 (MQ=255)
    gtgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAAt                                                              <  1:2550566/68‑1 (MQ=255)
    gtgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAAt                                                              <  1:875910/68‑1 (MQ=255)
    gtgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAAt                                                              <  1:2328728/68‑1 (MQ=255)
    gtgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAAt                                                              <  1:545346/68‑1 (MQ=255)
     tgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCa                                                            <  1:1675972/69‑1 (MQ=255)
     tgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCa                                                            <  1:815970/69‑1 (MQ=255)
     tgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCa                                                            <  1:2544501/69‑1 (MQ=255)
     tgtCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCa                                                            <  1:1994444/69‑1 (MQ=255)
      gtcgtcGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCa                                                            <  1:1650452/68‑1 (MQ=255)
      gtcgtcGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCa                                                            <  1:550554/68‑1 (MQ=255)
       tcgtcgGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAg                                                           >  1:3405183/1‑68 (MQ=255)
       tcgtcgGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAg                                                           >  1:2968659/1‑68 (MQ=255)
                    aGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:2108813/69‑1 (MQ=255)
                    aGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:1300182/69‑1 (MQ=255)
                    aGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:1840967/69‑1 (MQ=255)
                    aGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:1089070/69‑1 (MQ=255)
                    aGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:319913/69‑1 (MQ=255)
                    aGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:1446848/69‑1 (MQ=255)
                     gCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:1621640/68‑1 (MQ=255)
                     gCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAACGCAATCAGTTTACCCAGCTTCa                                             <  1:2149614/68‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:3211731/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:2780759/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:1111208/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:1017332/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:3132050/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:3142265/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:3180022/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:1589947/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:886400/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:2509555/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:670607/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:1409405/69‑1 (MQ=255)
                       cTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCg                                          <  1:659556/69‑1 (MQ=255)
                                 aCCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGc                                   >  1:30978/1‑66 (MQ=255)
                                 aCCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGc                                   >  1:3062588/1‑66 (MQ=255)
                                 aCCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGc                                   >  1:3187446/1‑66 (MQ=255)
                                       gATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCa                          >  1:2227559/1‑69 (MQ=255)
                                       gATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCa                          >  1:2450667/1‑69 (MQ=255)
                                                aCCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGt                  >  1:1168227/1‑68 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCGGAGAGCAAACTTCGTGGga              <  1:288021/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTTGTGGga              <  1:437163/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTTGga              <  1:802474/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:3416682/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:401306/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:718469/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:757633/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:945154/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:3429885/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2022656/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:1074990/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:135/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:1700254/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:1702154/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:1708131/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:1732359/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:1933503/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2265405/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2277292/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2457545/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2582058/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2582570/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2620425/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2721012/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2755591/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2864207/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:2877343/69‑1 (MQ=255)
                                                   gTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGga              <  1:3020506/69‑1 (MQ=255)
                                                        cATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATg          <  1:741632/68‑1 (MQ=255)
                                                              aGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTcc    >  1:2355014/1‑68 (MQ=255)
                                                              aGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTcc    >  1:3176986/1‑68 (MQ=255)
                                                              aGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTcc    >  1:562251/1‑68 (MQ=255)
                                                              aGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTcc    >  1:1947811/1‑68 (MQ=255)
                                                              aGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTcc    >  1:1334560/1‑68 (MQ=255)
                                                               gAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTCcat  <  1:601980/69‑1 (MQ=255)
                                                                  |                                                                 
TGCGGTGTCGTCGGTGAACCAGCCTTCAACGTGACCATCGATAGAAATACCGTTGTCATCGTAGAATGCAATCAGTTTACCCAGCTTCAGCGTACCCGCCAGAGAGCAAACTTCGTGGGAGATGCCTTCCAT  >  minE/1968024‑1968155

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