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 1,924,968 A→C 35.2% D323E (GAT→GAG)  lysA ← diaminopimelate decarboxylase, PLP‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,924,9680AC35.2% 62.8 / 73.6 88D323E (GAT→GAG) lysAdiaminopimelate decarboxylase, PLP‑binding
Reads supporting (aligned to +/- strand):  ref base A (6/51);  new base C (23/8);  total (29/59)
Fisher's exact test for biased strand distribution p-value = 1.97e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCACATAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATCAGATCGTTGAA  >  minE/1924909‑1925033
                                                           |                                                                 
tCACATAACGGCCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGCCCCTCAGCTGcc                                                          >  1:2235574/1‑69 (MQ=255)
tCACATAACGGCCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCCTCAGCTGcc                                                          >  1:3261430/1‑69 (MQ=255)
tCACATAACGGCCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCCTCAGCTGcc                                                          >  1:2721647/1‑69 (MQ=255)
tCACATAACGGCCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCCTCAGCTGcc                                                          >  1:790344/1‑69 (MQ=255)
tCACATAACGGCCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCCTCAGCTGcc                                                          >  1:1521319/1‑69 (MQ=255)
   caTAACGGTCC‑‑AGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:2983830/68‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:453020/69‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:2916216/69‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:1665308/69‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:57076/69‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:629528/69‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:1477934/69‑1 (MQ=255)
    aTAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAggg                                                      <  1:1284531/69‑1 (MQ=255)
          gTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:706200/69‑1 (MQ=255)
          gTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:2668428/69‑1 (MQ=255)
          gTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:1760217/69‑1 (MQ=255)
          gTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:2917759/69‑1 (MQ=255)
           tCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:1756557/68‑1 (MQ=255)
           tCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:2583988/68‑1 (MQ=255)
           tCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGa                                                <  1:2489254/68‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:1022684/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:2687363/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:2218205/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:2404811/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:3035739/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:3297129/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:751265/69‑1 (MQ=255)
             cGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGatat                                             <  1:942153/69‑1 (MQ=255)
               gagacgacGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATAtgg                                           >  1:1840785/3‑69 (MQ=255)
               gCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATAtgg                                           >  1:3206086/1‑69 (MQ=255)
               gCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATAtgg                                           >  1:1241696/1‑69 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATAtggtgtt                                       <  1:2597738/69‑3 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:3253579/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:3385072/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:432525/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:443557/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:993266/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:1983430/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:2375812/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:2088922/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:1793159/69‑1 (MQ=255)
                   cgacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:1764664/69‑1 (MQ=255)
                   cgacgGTTTACACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:3273315/69‑1 (MQ=255)
                    gacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:1197155/68‑1 (MQ=255)
                    gacgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:3389038/68‑1 (MQ=255)
                     acgGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATggtggt                                       <  1:1392959/67‑1 (MQ=255)
                        gTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:1740759/69‑1 (MQ=255)
                        gTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:368653/69‑1 (MQ=255)
                        gTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:2133610/69‑1 (MQ=255)
                        gTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:1608405/69‑1 (MQ=255)
                        gTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:1359086/69‑1 (MQ=255)
                        gTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:3028361/69‑1 (MQ=255)
                         tttCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTa                                  <  1:2332294/68‑1 (MQ=255)
                         tttCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTAc                                 <  1:2181328/69‑1 (MQ=255)
                         tttCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTAc                                 <  1:473043/69‑1 (MQ=255)
                          ttCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATAtggt                                          >  1:3260447/1‑59 (MQ=255)
                          ttCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATAtgg                                           >  1:3424155/1‑58 (MQ=255)
                                            ttCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:1520591/1‑67 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTTATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:2428748/68‑1 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAAGTACCGTACATTGCCGGGCGCATc             <  1:2859948/68‑1 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:1688774/68‑1 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:2048698/68‑1 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:1975294/68‑1 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:360890/68‑1 (MQ=255)
                                              ccAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:2113973/68‑1 (MQ=255)
                                               cAGAGAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATc             <  1:3238559/67‑1 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:2639999/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:2761489/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:1572206/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:154959/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:745933/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:2597879/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:846741/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:905154/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:135712/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:244641/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:458599/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:2660923/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:343608/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:3297085/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:3009881/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:322893/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:3207924/1‑63 (MQ=255)
                                                agagAACGACCCTCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGgcgc                >  1:2022126/1‑63 (MQ=255)
                                                  ataaCGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTAc                                 <  1:2261858/42‑1 (MQ=255)
                                                        aCCATCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATCAGATCGTTGaa  <  1:2951328/69‑1 (MQ=255)
                                                        aCCATCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATCAGATCGTTGaa  <  1:2448006/69‑1 (MQ=255)
                                                        aCCATCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATCAGATCGTTGaa  <  1:3033557/69‑1 (MQ=255)
                                                           |                                                                 
TCACATAACGGTCCGGCGACGACGGTTTCCACCGTTGGCGCGTGTTCCAGAGAACGACCATCAGCTGCCAGGGCACTGATATGGTGGTAACTACCGTACATTGCCGGGCGCATCAGATCGTTGAA  >  minE/1924909‑1925033

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A