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 1,463,756 C→A 40.6% L147L (CTG→CTT)  yfaA ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,463,7560CA40.6% 62.6 / 79.8 91L147L (CTG→CTT) yfaAhypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/29);  new base A (13/24);  total (38/53)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTG  >  minE/1463691‑1463818
                                                                 |                                                              
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:1160907/1‑69 (MQ=255)
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:1485084/1‑69 (MQ=255)
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:153070/1‑69 (MQ=255)
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:1548320/1‑69 (MQ=255)
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:1680685/1‑69 (MQ=255)
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:3024394/1‑69 (MQ=255)
tGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGc                                                             >  1:1298944/1‑69 (MQ=255)
    tGTCGCTGGTAGCTGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:1525801/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:2961416/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:2689080/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:1815710/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:1758338/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:3092005/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:1554593/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:431025/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:909113/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:983732/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:1419188/67‑1 (MQ=255)
    tGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCAc                                                           <  1:1403675/67‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:226268/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:651597/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      >  1:2812844/1‑64 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:1219266/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:1627555/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:1710191/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:1727981/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:3392614/64‑1 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      >  1:3224817/1‑64 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      >  1:1807148/1‑64 (MQ=255)
            gTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCatat                                                      <  1:944771/64‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:2653749/69‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:2297068/69‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:3028925/69‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:1926200/69‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:397961/69‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:651989/69‑1 (MQ=255)
              aGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:655996/69‑1 (MQ=255)
               gCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGa                                               <  1:325227/68‑1 (MQ=255)
                 ggCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGaaa                                             <  1:2734301/68‑1 (MQ=255)
                       caacaaTGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGcc                                      >  1:1765460/1‑69 (MQ=255)
                       caacaaTGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGcc                                      >  1:2033875/1‑69 (MQ=255)
                       caacaaTGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGcc                                      >  1:633476/1‑69 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                         <  1:3096842/68‑2 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                         <  1:2963538/68‑2 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                         <  1:2392625/68‑2 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                         <  1:1156007/68‑2 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                         <  1:2164166/68‑2 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:1952337/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:1456644/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:780786/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:2532600/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:3118967/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:1452808/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:2154192/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:14162/68‑1 (MQ=255)
                                     gcagTTTGCTTAAACCACTGCGCTGGATAAGCAACATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:815617/68‑1 (MQ=255)
                                      cagTTTGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATGc                         <  1:2198142/67‑1 (MQ=255)
                                           tGCTTAGACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:442337/1‑53 (MQ=255)
                                           tGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAgcg                  >  1:160417/1‑69 (MQ=255)
                                           tGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAgcg                  >  1:68003/1‑69 (MQ=255)
                                           tGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTACCACAgcg                  >  1:2358785/1‑69 (MQ=255)
                                           tGCTTAAACCACTGCGCTGGATAAGTACCATATAATGTGAAAGATGACCTTGt                                  >  1:1385678/1‑53 (MQ=38)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATga                                        >  1:3039310/1‑46 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTg                                   >  1:1228194/1‑52 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:1479937/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:331469/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:1793206/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:1311920/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:3022761/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:1314167/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:2943519/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:2642370/1‑53 (MQ=39)
                                           tGCTTAAACCACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGt                                  >  1:1992293/1‑53 (MQ=39)
                                                   ccACTGCGCTGGATAAGCACCATATAATGTGAAAGATGACCTTGTTTATCATga                         <  1:1563573/54‑2 (MQ=255)
                                                    cACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcg         >  1:834803/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:1426978/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:2297112/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:2278212/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:911224/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:1177003/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:1602883/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:1698007/1‑69 (MQ=255)
                                                     aCTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTgcgc        >  1:334675/1‑69 (MQ=255)
                                                           cTGTATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:398018/69‑1 (MQ=255)
                                                           cTGGATCAGCACCATATAATGTGAAAGATGGCCTTTTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:927668/69‑1 (MQ=255)
                                                           cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:2465667/69‑1 (MQ=255)
                                                           cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:2397379/69‑1 (MQ=255)
                                                           cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:2261036/69‑1 (MQ=255)
                                                           cTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:95702/69‑1 (MQ=255)
                                                            tGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:2586434/68‑1 (MQ=255)
                                                            tGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTg  <  1:1868077/68‑1 (MQ=255)
                                                                 |                                                              
TGGCTGTCGCTGGTAGCGGCAAACAACAATGGCTCCAGCAGTTTGCTTAAACCACTGCGCTGGATCAGCACCATATAATGTGAAAGATGGCCTTGTTTATCGTGCCACAGCGCTGCCTGCGCGGGCTG  >  minE/1463691‑1463818

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