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
A11 F142 I0 R1 175 91.2 4812830 94.5% 4548124 99.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,436,937 A→T 100% D305E (GAT→GAA)  pdxB ← erythronate‑4‑phosphate dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,436,9370AT98.5% 216.0 / ‑3.9 65D305E (GAT→GAA) pdxBerythronate‑4‑phosphate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (36/28);  total (36/29)
Fisher's exact test for biased strand distribution p-value = 4.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.56e-01

ATCGAACTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGATCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTGCTATA  >  NC_000913/2436841‑2437032
                                                                                                |                                                                                               
aTCGAACTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCg                                                                                              <  2:1631109/100‑1 (MQ=255)
   gAACTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAg                                                                                            >  2:1978226/1‑99 (MQ=255)
   gAACTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGc                                                                                           >  1:2253772/1‑100 (MQ=255)
      cTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCggg                                                                                        >  2:1698350/1‑100 (MQ=255)
      cTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCggg                                                                                        >  2:1547723/1‑100 (MQ=255)
        cACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGcc                                                                                      <  2:1128794/100‑1 (MQ=255)
        cACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGcc                                                                                      >  2:632242/1‑100 (MQ=255)
          ccgggTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGATCGAGCGGGCCAt                                                                                    <  1:1944316/97‑1 (MQ=255)
                 tCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGt                                                                             <  2:939489/100‑1 (MQ=255)
                     ggCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATg                                                                         <  1:298189/100‑1 (MQ=255)
                      gctaCTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGc                                                                        <  1:1240215/97‑1 (MQ=255)
                      gCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGc                                                                        <  1:756601/100‑1 (MQ=255)
                         aCTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGAc                                                                     <  1:1698370/100‑1 (MQ=255)
                         aCTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGAc                                                                     <  2:846549/100‑1 (MQ=255)
                         aCTCTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGTTTGTTCGAGCGGGCCATGCAGCGTAATGCGAc                                                                     <  2:2239725/100‑1 (MQ=255)
                          cTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGAcc                                                                    >  1:2016632/1‑100 (MQ=255)
                          cTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGAcc                                                                    >  1:845293/1‑100 (MQ=255)
                          cTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGAcc                                                                    >  1:701383/1‑100 (MQ=255)
                            ttACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCaa                                                                  >  1:2330083/1‑100 (MQ=255)
                               cGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAAct                                                               >  1:500082/1‑100 (MQ=255)
                               cGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAAct                                                               >  1:979760/1‑100 (MQ=255)
                                 cAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAActct                                                             <  2:2140268/100‑1 (MQ=255)
                                 cAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAActct                                                             >  2:764291/1‑100 (MQ=255)
                                  aGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTg                                                            <  1:722383/100‑1 (MQ=255)
                                     ggTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGgcg                                                         <  1:433994/100‑1 (MQ=255)
                                        gCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcag                                                      <  1:24040/100‑1 (MQ=255)
                                        gCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcag                                                      <  2:1341521/100‑1 (MQ=255)
                                          gTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcaggc                                                    >  2:1602990/1‑100 (MQ=255)
                                          gTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcaggc                                                    >  2:518445/1‑100 (MQ=255)
                                          gTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcaggc                                                    >  1:1359342/1‑100 (MQ=255)
                                           tCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcaggca                                                   >  1:1203052/1‑100 (MQ=255)
                                            cATCGCGGCGCACATCATACACAAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCgcaggcag                                                  >  2:1391023/1‑100 (MQ=255)
                                                 cggcgCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATg                                             >  2:661473/1‑100 (MQ=255)
                                                  ggagtacaTTATCCACCAATTGCACCAGCCTTTTTATTCTCGGTTGTTCGAGTGGGCGATGTAGCGTAATGCGATCAAATTCTGGCGCAGGCAGTAATg                                             <  2:228034/94‑1 (MQ=255)
                                                     gcACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATc                                         <  2:2086214/100‑1 (MQ=255)
                                                       acaTCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCa                                       >  2:1177529/1‑100 (MQ=255)
                                                       acaTCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCa                                       >  1:1894230/1‑100 (MQ=255)
                                                       acaTCATACACCAAATGCACCAGCCTTTTAAGCGTCAGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCa                                       >  2:188302/1‑100 (MQ=255)
                                                          tcatACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAgcg                                    >  2:492556/1‑100 (MQ=255)
                                                          tcatACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAgcg                                    >  1:2106079/1‑100 (MQ=255)
                                                           catACACCAAGTGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGCGCCATGCATCGTAATGCGACCAAACTCTGGCTCAGGCAGTAATGTATCCAgcgc                                   <  2:544586/100‑1 (MQ=255)
                                                           catACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAgcgc                                   >  2:2255152/1‑100 (MQ=255)
                                                               cacCATGTGCGCCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAgc                                     <  2:2332504/94‑1 (MQ=255)
                                                               cacCAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATGCAGCGCAACg                               <  2:1688483/100‑1 (MQ=255)
                                                               cacCAAATGCACCAGCCTTTTCAGCGTCGGTTGTGCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCCGCGCCACg                               >  1:1295009/1‑100 (MQ=255)
                                                                  cAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGc                            <  2:1425669/100‑1 (MQ=255)
                                                                  cAAATGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGAGCAACGTGc                            >  2:876427/1‑100 (MQ=255)
                                                                   aaaTGCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCt                           >  2:1556719/1‑100 (MQ=255)
                                                                       gCACCAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTc                       <  2:2339034/100‑1 (MQ=255)
                                                                          ccAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCGGTAATGTATCCAGCGCAACGTGCTGTTCATg                    >  1:485369/1‑100 (MQ=255)
                                                                          ccAGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATg                    >  1:886801/1‑100 (MQ=255)
                                                                            aGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGcc                  <  2:1894208/100‑1 (MQ=255)
                                                                            aGCCTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGcc                  <  2:902441/100‑1 (MQ=255)
                                                                              ccTTTTCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCa                <  1:2099599/100‑1 (MQ=255)
                                                                                ttttCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAAt              >  1:1956579/1‑100 (MQ=255)
                                                                                ttttCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAAt              <  2:1197640/100‑1 (MQ=255)
                                                                                ttttCAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAAt              >  1:1944405/1‑100 (MQ=255)
                                                                                    cAGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATaaa           >  2:1415189/1‑99 (MQ=255)
                                                                                    cAGCGGCGGTTGTTCGAGCGGGCCATGCTGCGTCATGCGACCTAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAAAGTGCTGTTCATGCCAAATa             <  2:619005/97‑1 (MQ=255)
                                                                                     aGCGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACt         >  1:1080614/1‑100 (MQ=255)
                                                                                       cGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTg       <  2:317037/100‑1 (MQ=255)
                                                                                       cGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTg       >  1:2383241/1‑100 (MQ=255)
                                                                                       cGTCGGTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTg       <  1:1263980/100‑1 (MQ=255)
                                                                                           ggTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTGCtat   >  2:182358/1‑100 (MQ=255)
                                                                                           ggTTGTTCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTGCtat   >  1:644264/1‑100 (MQ=255)
                                                                                            gttgttCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTGCtata  <  2:2016610/100‑1 (MQ=255)
                                                                                            gttgttCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTGCtata  <  2:1867562/100‑1 (MQ=255)
                                                                                                |                                                                                               
ATCGAACTCACCCGGTATCCCGGCGACTTTACGCAGCGGTGCGTCATCGCGGCGCACATCATACACCAAATGCACCAGCCTTTTCAGCGTCGGTTGATCGAGCGGGCCATGCAGCGTAATGCGACCAAACTCTGGCGCAGGCAGTAATGTATCCAGCGCAACGTGCTGTTCATGCCCAATAAACTTGCTATA  >  NC_000913/2436841‑2437032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A