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 2,387,276 G→A 100% L88L (CTG→TTG)  yigM ← predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,387,2760GA78.5% 99.7 / 20.2 74L88L (CTG→TTG) yigMpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (1/15);  new base A (0/58);  total (1/73)
Fisher's exact test for biased strand distribution p-value = 2.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATACATCACGCCAAGCTGC  >  minE/2387243‑2387340
                                 |                                                                
tGATGTAGAGCGGCGTCAGCACGGTGAATAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:687213/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:1497744/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:2127697/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:2567623/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:160849/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:2816346/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:3304881/69‑1 (MQ=255)
tGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGa                               <  1:1254154/69‑1 (MQ=255)
ggATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTAAGGTAGAGATAAGCGCGGa                               <  1:3023697/68‑1 (MQ=255)
 gATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGaa                              <  1:144482/69‑1 (MQ=255)
 gATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGaa                              <  1:1455363/69‑1 (MQ=255)
 gATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGaa                              <  1:3372046/69‑1 (MQ=255)
  aTGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGaa                              <  1:777646/68‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:3285856/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:3199601/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:586046/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2497249/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2580579/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2593105/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:3318731/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2931961/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:3296891/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2946334/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2040935/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:1475026/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:1439067/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:907562/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:1285806/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:186312/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:1919035/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:1129986/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:107136/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:855906/69‑1 (MQ=255)
     tAGAGCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAAACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:2960582/69‑1 (MQ=255)
      agagCGGCGTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:703765/68‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2334987/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2966398/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:1484913/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2934917/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:1538051/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2913255/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:1409859/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:1970006/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2728310/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:1587795/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:749984/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:3139214/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2265737/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:2420483/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:3149332/69‑1 (MQ=255)
           ggcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:1929907/69‑1 (MQ=255)
            gcgTCAGTACGGTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCata                    <  1:296868/68‑1 (MQ=255)
               tCAGCACGGTGCACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATAc                 >  1:1774981/1‑68 (MQ=255)
                cAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATACAt               <  1:2118656/69‑1 (MQ=255)
                 aGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATACAt               <  1:2574987/68‑1 (MQ=255)
                      ggTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTc                          <  1:697565/52‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:3421309/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:49005/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:856805/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:639143/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:682923/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:1090845/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:3028833/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:1540809/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:1660569/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:1971881/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2143158/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2228483/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2333842/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2438387/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2891555/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2917987/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:2989260/68‑1 (MQ=255)
                       gTGAACAGCAACAGTTCGGAGACCGTCAGGTAGAGATAGGCGCGGAAACTCAGCATATACATCACAcc         <  1:3093617/68‑1 (MQ=255)
                            cagcagcagCTCGGAAACCGTCAGGTAGAGATAAg                                     >  1:2337741/1‑35 (MQ=255)
                            cagcagcagCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAg                        >  1:2282041/1‑48 (MQ=255)
                            cagcagcagCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAg                        >  1:2272342/1‑48 (MQ=255)
                            cagcagcagCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAg                        >  1:3356442/1‑48 (MQ=255)
                            cagcagcagCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAg                        >  1:870048/1‑48 (MQ=255)
                             agcagcagcTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATACATCACGCCAAGCTGc  <  1:2380414/69‑1 (MQ=255)
                             agcagcagcTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATACATCACGCCAAGCTGc  <  1:922285/69‑1 (MQ=255)
                                 |                                                                
TGATGTAGAGCGGCGTCAGCACGGTGAACAGCAGCAGCTCGGAAACCGTCAGGTAGAGATAAGCGCGGAAACTCAGCATATACATCACGCCAAGCTGC  >  minE/2387243‑2387340

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