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 2,248,786 T→C 27.7% L202L (TTG→CTG)  thiE → thiamin phosphate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,248,7860TC27.7% 93.5 / 37.2 90L202L (TTG→CTG) thiEthiamin phosphate synthase
Reads supporting (aligned to +/- strand):  ref base T (24/41);  new base C (4/21);  total (28/62)
Fisher's exact test for biased strand distribution p-value = 7.52e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCAGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACTTTATGCGTTATAGCCGCCAAA  >  minE/2248723‑2248847
                                                               |                                                             
ggCAGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGc                                                            >  1:1877577/1‑67 (MQ=255)
ggCAGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGc                                                            >  1:3392109/1‑67 (MQ=255)
ggCAGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCt                                                           >  1:400941/1‑68 (MQ=255)
ggCAGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGAAGACTGGCGTTTGGCAACGGCACAGTTGCt                                                           >  1:2315306/1‑68 (MQ=255)
   aGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaa                                                       <  1:2140708/69‑1 (MQ=255)
   aGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaa                                                       <  1:3062059/69‑1 (MQ=255)
   aGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaa                                                       <  1:2015386/69‑1 (MQ=255)
   aGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaa                                                       <  1:1675036/69‑1 (MQ=255)
   aGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaa                                                       <  1:361792/69‑1 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:1873523/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:3393661/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:1740586/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:1736800/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:1980943/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:1555453/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:1493276/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:2142856/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:2981000/1‑69 (MQ=255)
    gTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGaaa                                                      >  1:2466547/1‑69 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGTTGGa                                                        <  1:256141/64‑1 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGTTGGa                                                        <  1:3416988/64‑1 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGTTGGa                                                        <  1:570107/64‑1 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGTTGGa                                                        <  1:35168/64‑1 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGTTGGa                                                        <  1:477531/64‑1 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGa                                                        >  1:2782446/1‑64 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGa                                                        >  1:2350697/1‑64 (MQ=255)
       tCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAAt                                                     >  1:1827543/1‑67 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:1379529/1‑68 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:920288/1‑68 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:3115016/1‑68 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:1548273/1‑68 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:346355/1‑68 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:1751051/1‑68 (MQ=255)
         gCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGc                                                  >  1:1876086/1‑68 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAgg                                               <  1:3067175/69‑1 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAgg                                               <  1:38513/69‑1 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAgg                                               <  1:2842193/69‑1 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAgg                                               <  1:1234047/69‑1 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAgg                                               <  1:1840333/69‑1 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAg                                                <  1:2150651/68‑1 (MQ=255)
           cgtcgtCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAg                                                <  1:1203556/68‑1 (MQ=255)
            gtcgtcAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAgg                                               <  1:2478233/68‑1 (MQ=255)
                   gcgcCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAgctgct                                                           >  1:2640630/1‑49 (MQ=255)
                   gcgcCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGc                                        >  1:2685866/1‑68 (MQ=255)
                   gcgcCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCg                                       >  1:659502/1‑69 (MQ=255)
                   gcgcCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCg                                       >  1:299108/1‑69 (MQ=255)
                   gcgcCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCg                                       >  1:2294825/1‑69 (MQ=255)
                      ccATTACTCAAGCCGCAGACTTGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2979391/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2128101/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2601377/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2021909/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:3083963/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:3151286/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:3215256/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:3359082/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2000965/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:1868440/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:1354908/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:505551/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:538817/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:557259/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:272241/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2386423/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2836625/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2824849/69‑1 (MQ=255)
                      ccATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2703875/69‑1 (MQ=255)
                       cATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:2840418/68‑1 (MQ=255)
                         ttACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGCTGCTGGAAATTGCAGGAGTTGGCGatg                                    <  1:1622211/66‑1 (MQ=255)
                             tCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGAc                              <  1:133692/68‑1 (MQ=255)
                             tCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGAc                              <  1:1354694/68‑1 (MQ=255)
                             tCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGAc                              <  1:192862/68‑1 (MQ=255)
                              cAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGAc                              <  1:1598311/67‑1 (MQ=255)
                              cAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGAc                              <  1:2822502/67‑1 (MQ=255)
                              cAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGAc                              <  1:458221/67‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:2157535/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:1157547/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:2586000/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:714135/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:513834/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:720494/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:813494/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:490997/69‑1 (MQ=255)
                                    gCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:1448007/69‑1 (MQ=255)
                                     cAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:1697834/68‑1 (MQ=255)
                                     cAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:2799061/68‑1 (MQ=255)
                                     cAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:3136755/68‑1 (MQ=255)
                                                        ggCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACTTTATGCGTTATAGCCGCCaaa  <  1:2792289/69‑1 (MQ=255)
                                                        ggCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACTTTATGCGTTATAGCCGCCaaa  <  1:2017439/69‑1 (MQ=255)
                                                        ggCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACTTTATGCGTTATAGCCGCCaaa  <  1:3023119/69‑1 (MQ=255)
                                                        ggCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACTTTATGCGTTATAGCCGCCaaa  <  1:1163731/69‑1 (MQ=255)
                                                         gCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACtt                      <  1:44224/48‑1 (MQ=255)
                                                               |                                                             
GGCAGTATCGCCGTCGTCAGCGCCATTACTCAAGCCGCAGACTGGCGTTTGGCAACGGCACAGTTGCTGGAAATTGCAGGAGTTGGCGATGAATGACCGTGACTTTATGCGTTATAGCCGCCAAA  >  minE/2248723‑2248847

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A