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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,691,217 G→A 10.4% A310T (GCA→ACA)  manA → mannose‑6‑phosphate isomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,691,2170GA10.4% 203.1 / 11.0 67A310T (GCA→ACA) manAmannose‑6‑phosphate isomerase
Reads supporting (aligned to +/- strand):  ref base G (32/28);  new base A (5/2);  total (37/30)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

GGTTGCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATAAAGAAA  >  W3110S.gb/1691150‑1691286
                                                                   |                                                                     
ggTTGCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTCTTGACCCAGCCGGTGAAACAAGGTg                                                                       >  1:1799532/1‑68 (MQ=255)
 gTTGCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAg                                                                    <  1:2679431/70‑1 (MQ=255)
 gTTGCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAg                                                                    >  1:2382201/1‑70 (MQ=255)
   tGCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAAc                                                                 >  1:2523567/1‑71 (MQ=255)
    gCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAAc                                                                 <  1:3450560/70‑1 (MQ=255)
     ccAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGTTGCAGAACTg                                                               <  1:2074672/71‑1 (MQ=255)
     ccAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTACAGAACTg                                                               <  1:4448876/71‑1 (MQ=255)
        aTGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGAc                                                            >  1:2479861/1‑71 (MQ=255)
        aTGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGAc                                                            >  1:3872672/1‑71 (MQ=255)
        aTGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTACAGAACTGGAc                                                            >  1:1013731/1‑71 (MQ=255)
         tgtgAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACt                                                           >  1:3861518/1‑71 (MQ=255)
            gAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGa                                                             >  1:3016401/1‑66 (MQ=255)
             aaaTTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTg                                                               >  1:2407015/1‑63 (MQ=255)
              aaTTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTccc                                                       >  1:980711/1‑70 (MQ=255)
               aTTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACt                                                                >  1:2722894/1‑60 (MQ=255)
               aTTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGa                                                     >  1:4425922/1‑71 (MQ=255)
               aTTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTACAGAACTGGACTTCCCGa                                                     >  1:4196799/1‑71 (MQ=255)
                ttCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAGGGTGCAGAACt                                                                >  1:4615669/1‑59 (MQ=255)
                 tCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTccc                                                       <  1:1809272/67‑1 (MQ=255)
                 tCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGAtt                                                   >  1:250904/1‑71 (MQ=255)
                    aaGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTACAGAACTGGACTTCCCGATTCCa                                                <  1:4080089/71‑1 (MQ=255)
                       ccAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGa                                                                   <  1:3376492/49‑1 (MQ=255)
                         aaaCCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGga                                           >  1:3838533/1‑71 (MQ=255)
                         aaaCCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGga                                           >  1:3971585/1‑71 (MQ=255)
                           aCCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGgatg                                         <  1:1958895/71‑1 (MQ=255)
                               gCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGgatga                                        <  1:3577056/68‑1 (MQ=255)
                                 tAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTg                                   >  1:1835535/1‑71 (MQ=255)
                                 tAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTg                                   >  1:4596252/1‑71 (MQ=255)
                                  aaCCAGTTGTTGACCCAGCCGGTGAAACAAGGTACAGAACt                                                                >  1:3337260/1‑41 (MQ=255)
                                   aCCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGAt                                                    <  1:2896850/52‑1 (MQ=255)
                                   aCCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGcc                                 >  1:123502/1‑71 (MQ=255)
                                   aCCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGAATTTGcc                                 >  1:2153624/1‑71 (MQ=255)
                                    ccAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCg                                                      >  1:2191758/1‑49 (MQ=255)
                                     cAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGAtttt                                    >  1:2565796/1‑66 (MQ=255)
                                     cAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCtt                               >  1:3516018/1‑71 (MQ=255)
                                      aggtgttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtc                              <  1:1016373/68‑1 (MQ=255)
                                      aGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtc                              >  1:795124/1‑71 (MQ=255)
                                       gttgttGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtct                             <  1:121080/71‑1 (MQ=255)
                                        ttgttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtctc                            >  1:4350945/1‑71 (MQ=255)
                                        ttgttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtctc                            <  1:1078534/71‑1 (MQ=255)
                                         tgttgACGCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCg                           >  1:3291134/1‑71 (MQ=255)
                                         tgttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCg                           >  1:2457907/1‑71 (MQ=255)
                                         tgttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCg                           >  1:1023311/1‑71 (MQ=255)
                                         tgttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCg                           >  1:1562076/1‑71 (MQ=255)
                                          gttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCg                           <  1:2444517/70‑1 (MQ=255)
                                          gttgACCCAGCAGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGc                          >  1:1764975/1‑71 (MQ=255)
                                           ttgACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCt                         <  1:3795459/71‑1 (MQ=255)
                                            tgACCCAGCCGGTGAAACAAGGTACAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTg                        >  1:433069/1‑71 (MQ=255)
                                             gACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAg                                               <  1:1636883/47‑1 (MQ=255)
                                             gACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTg                        >  1:3494408/1‑70 (MQ=255)
                                              aCCCAGCCTGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGc                       <  1:4155546/70‑1 (MQ=255)
                                                 cAGCCGGTGAAACAAGGTACAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGa                   >  1:1851924/1‑71 (MQ=255)
                                                  aGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGAc                  >  1:1984754/1‑71 (MQ=255)
                                                        tGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtc                              <  1:3887695/53‑1 (MQ=255)
                                                          aaaCAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGc                                  <  1:259176/47‑1 (MQ=255)
                                                          aaaCAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTg                        <  1:3043587/57‑1 (MQ=255)
                                                          aaaCAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGa          >  1:1547331/1‑71 (MQ=255)
                                                           aaCAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGAt         <  1:4080770/71‑1 (MQ=255)
                                                            aCAAGGTGCAGAACTGGACTTCCCGATTCCAGTTGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGAt         >  1:2495168/1‑70 (MQ=255)
                                                             cAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGa                   <  1:4113691/59‑1 (MQ=255)
                                                             cAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATaa       <  1:3260928/71‑1 (MQ=255)
                                                              aaGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATaat      <  1:1034608/71‑2 (MQ=255)
                                                               aGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTtctc                            <  1:3683011/48‑1 (MQ=255)
                                                                 gTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATAAAGaa   <  1:2776334/71‑1 (MQ=255)
                                                                 gTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATAAAGaa   <  1:686237/71‑1 (MQ=255)
                                                                  tGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCtt               <  1:3084524/58‑1 (MQ=255)
                                                                  tGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATAAAGaaa  <  1:698559/71‑1 (MQ=255)
                                                                  tGCAGAACTGGACTTCACGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATg                    <  1:1041710/53‑1 (MQ=255)
                                                                   |                                                                     
GGTTGCCAATGTGAAATTCGAAGCCAAACCGGCTAACCAGTTGTTGACCCAGCCGGTGAAACAAGGTGCAGAACTGGACTTCCCGATTCCAGTGGATGATTTTGCCTTCTCGCTGCATGACCTTAGTGATAAAGAAA  >  W3110S.gb/1691150‑1691286

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