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 1,274,978 A→G 25.8% T97A (ACA→GCA)  yodA → conserved metal‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,274,9780AG25.8% 166.8 / 56.4 143T97A (ACA→GCA) yodAconserved metal‑binding protein
Reads supporting (aligned to +/- strand):  ref base A (40/66);  new base G (19/18);  total (59/84)
Fisher's exact test for biased strand distribution p-value = 1.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

Only 100 of 148 total aligned reads displayed.

CGTCTTTCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCATTGTTGAATTCCATAGAAATA  >  minE/1274913‑1275046
                                                                 |                                                                    
cGTCTTTCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATcac                                                                     >  1:1529343/1‑67 (MQ=255)
cGTCTTTCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACaa                                                                   >  1:1257624/1‑69 (MQ=255)
cGTCATTCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACaa                                                                   >  1:1985755/1‑69 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               >  1:2347587/1‑69 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               <  1:1159747/69‑1 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               >  1:153975/1‑69 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               >  1:3367110/1‑69 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               >  1:537630/1‑69 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               <  1:3013311/69‑1 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               <  1:1686051/69‑1 (MQ=255)
    tttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               <  1:60578/69‑1 (MQ=255)
     ttCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGt                                                               <  1:426999/68‑1 (MQ=255)
        agaagaAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:2743233/67‑1 (MQ=255)
        agaagaAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:495256/67‑1 (MQ=255)
        agaagaAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:530253/67‑1 (MQ=255)
        agaagaAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:1290753/67‑1 (MQ=255)
        agaagaAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:3327761/67‑1 (MQ=255)
        agaagaAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:3030062/67‑1 (MQ=255)
         gaagaaAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTa                                                             <  1:873007/66‑1 (MQ=255)
           agaaAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGc                                                          >  1:933590/1‑67 (MQ=255)
           agaaAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGc                                                          >  1:2161161/1‑67 (MQ=255)
           agaaAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGc                                                          >  1:923791/1‑67 (MQ=255)
           agaaAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGc                                                          >  1:621230/1‑67 (MQ=255)
           agaaAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGc                                                          >  1:1082175/1‑67 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:828405/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:1200910/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:3216348/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:1985674/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:1945292/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:1580154/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:2651616/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:24220/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:2487247/69‑1 (MQ=255)
                     tGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCga                                              <  1:255025/69‑1 (MQ=255)
                        aGATAAATCTAAAACTTTTGCTGAAATTAAAGATTATTATCAGAAAGGt                                                               <  1:37124/49‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:7594/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:78347/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:3094676/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:1239836/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:1358915/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:1634266/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:439460/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:1405973/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:1451698/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatg                                          <  1:1483772/69‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           <  1:1479297/68‑1 (MQ=255)
                         gATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           <  1:2762984/68‑1 (MQ=255)
                           taaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:2965257/1‑66 (MQ=255)
                           taaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:446633/1‑66 (MQ=255)
                           taaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:2518486/1‑66 (MQ=255)
                           taaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:524003/1‑66 (MQ=255)
                           taaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:1974641/1‑66 (MQ=255)
                           taaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:1180766/1‑66 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:1026094/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:2545389/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:2010501/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:3215114/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:3142383/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:482836/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:2880208/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:237822/63‑1 (MQ=255)
                           taaaaccaaaacATTTGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:1028198/63‑1 (MQ=255)
                           taaaaccaaaacATATGCTGAAATTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCga                                              <  1:1414598/63‑1 (MQ=255)
                            aaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatgat                                        >  1:1253383/1‑68 (MQ=255)
                            aaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgatgat                                        >  1:79171/1‑68 (MQ=255)
                            aaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGAtt                                       >  1:110127/1‑69 (MQ=255)
                            aaaactaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGAtt                                       >  1:359513/1‑69 (MQ=255)
                               actaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTgg                                     <  1:1398409/68‑1 (MQ=255)
                               actaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTgg                                     <  1:300029/68‑1 (MQ=255)
                               actaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTgg                                     <  1:1548962/68‑1 (MQ=255)
                               actaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTgg                                     <  1:3017327/68‑1 (MQ=255)
                               actaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTgg                                     <  1:3185841/68‑1 (MQ=255)
                               actaaaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGc                                    >  1:2916760/1‑69 (MQ=255)
                                   aaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:672958/1‑58 (MQ=255)
                                   aaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:3430050/1‑58 (MQ=255)
                                   aaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:2623321/1‑58 (MQ=255)
                                   aaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:217681/1‑58 (MQ=255)
                                   aaacATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAgat                                           >  1:2294725/1‑58 (MQ=255)
                                           gCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCgt                                              <  1:2136443/47‑2 (MQ=255)
                                              gAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCAt                      <  1:2085407/68‑1 (MQ=255)
                                              gAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCAt                      <  1:1621422/68‑1 (MQ=255)
                                              gAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCAt                      <  1:1172975/68‑1 (MQ=255)
                                              gAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCAt                      <  1:2197176/68‑1 (MQ=255)
                                              gAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCAt                      <  1:2818990/68‑1 (MQ=255)
                                              gAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCAt                      <  1:2276892/68‑1 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:2079384/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:1010053/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:258529/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:2726853/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:1232529/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:750818/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:672489/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:1291302/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:463005/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:1908812/1‑69 (MQ=255)
                                               aaaTTAAAGATTATTATCGCAAAGGTTATGCGACAGATATCGAAATGATTGGCATTGAGGACGGCAttg                    >  1:2004338/1‑69 (MQ=255)
                                                    aaaGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCATTGTTGaa               >  1:1370561/1‑69 (MQ=255)
                                                             tatCACAAAGGTTATGCAACAGATATCGAGATGATTgg                                     <  1:2918431/38‑1 (MQ=255)
                                                                 acaAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCATTGTTGAATTCCATAGAaata  >  1:1560970/1‑69 (MQ=255)
                                                                 acaAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCATTGTTGAATTCCATAGAaata  >  1:425358/1‑69 (MQ=255)
                                                                 |                                                                    
CGTCTTTCAGAAGAAAGCGGATGCAGATAAAACTAAAACATTTGCTGAAATTAAAGATTATTATCACAAAGGTTATGCAACAGATATCGAGATGATTGGCATTGAGGACGGCATTGTTGAATTCCATAGAAATA  >  minE/1274913‑1275046

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