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
A1 F21 I0 R1 476 35.3 2812105 96.7% 2719305 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,125,813 C→T 15.8% P152L (CCT→CTT)  rpe → D‑ribulose‑5‑phosphate 3‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,125,8130CT15.8% 146.0 / 17.9 57P152L (CCT→CTT) rpeD‑ribulose‑5‑phosphate 3‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (23/25);  new base T (4/5);  total (27/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01

GATGGATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGACTAG  >  W3110S.gb/4125745‑4125881
                                                                    |                                                                    
gATGGATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCt                                                                     >  1:1353951/1‑70 (MQ=255)
 aTGGATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCa                                                                   <  1:490249/71‑1 (MQ=255)
   ggATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCaaa                                                                 >  1:1162674/1‑71 (MQ=255)
    gATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGTTCAGTCTTTCATTCTTCa                                                                   <  1:287901/68‑1 (MQ=255)
    gATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCTTCaaa                                                                 >  1:1144623/1‑70 (MQ=255)
    gATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCaaa                                                                 <  1:84542/70‑1 (MQ=255)
    gATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCaaa                                                                 >  1:1640912/1‑70 (MQ=255)
           tGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCa                                                                   <  1:1886200/61‑1 (MQ=255)
           tGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCa                                                                   <  1:1796451/61‑1 (MQ=255)
             gATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATa                                                        <  1:1245703/70‑1 (MQ=255)
             gATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATa                                                        <  1:1342803/70‑1 (MQ=255)
               tgtgATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAAc                                                     >  1:1055943/1‑71 (MQ=255)
                   aTCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTgcg                                                 >  1:1871781/1‑71 (MQ=255)
                     ccTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGa                                                          >  1:2056424/1‑60 (MQ=255)
                     ccTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTgcg                                                 >  1:2807724/1‑69 (MQ=255)
                         ctgATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAg                                            >  1:1020393/1‑70 (MQ=255)
                            aTGTCCGTCAACCCTGGTTTCGGCTGTCAGTCTTTCATTCTTCAAACACTGGATAAACTGCGCGAAGTACg                                        >  1:638626/1‑71 (MQ=39)
                             tGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCa                                                                   <  1:2741623/43‑1 (MQ=255)
                             tGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCa                                                                   <  1:1297565/43‑1 (MQ=255)
                                  gTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCa                                                                   <  1:119100/38‑1 (MQ=255)
                                   tCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCTTCAAACACTGGATAAACTGcgcg                                               <  1:363953/57‑1 (MQ=255)
                                    cAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCaaa                                                                 >  1:2182687/1‑38 (MQ=255)
                                    cAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTa                                >  1:2557778/1‑71 (MQ=255)
                                    cAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTa                                >  1:782445/1‑71 (MQ=255)
                                     aaCCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTAt                               >  1:2341350/1‑71 (MQ=255)
                                      aCCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATc                              <  1:789649/71‑1 (MQ=255)
                                         cTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTg                                                            >  1:526733/1‑38 (MQ=255)
                                         cTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTg                                                            >  1:491624/1‑38 (MQ=255)
                                         cTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcgac                           <  1:2136599/71‑1 (MQ=255)
                                           ggTTTCGGCGGTCAGTCTTTCATTCTTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcgac                           >  1:589329/1‑69 (MQ=255)
                                           ggTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcgac                           >  1:2113886/1‑69 (MQ=255)
                                            gattCGGCGGTCAGTCTTTCATTACTCAAACACTGGATaa                                                       <  1:199509/38‑1 (MQ=255)
                                            gTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTa                                          >  1:477700/1‑53 (MQ=255)
                                                    ggTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCtt                <  1:1087769/71‑1 (MQ=255)
                                                        aGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAg                        <  1:2231418/59‑1 (MQ=255)
                                                        aGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGa             <  1:2500366/70‑1 (MQ=255)
                                                        aGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGa             <  1:1366465/70‑1 (MQ=255)
                                                        aGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGa             <  1:907243/70‑1 (MQ=255)
                                                         gTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAg                                            <  1:2322879/38‑1 (MQ=255)
                                                         gTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGt                                           <  1:1674568/39‑1 (MQ=255)
                                                          tCTTTCATTCTTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcgac                           <  1:1273981/54‑1 (MQ=255)
                                                          tCTTTCATTCTTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcgac                           <  1:1758384/54‑1 (MQ=255)
                                                          tCTTTCATTCTTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcgac                           <  1:1360532/54‑1 (MQ=255)
                                                          tCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAg                        <  1:126327/57‑1 (MQ=255)
                                                            tttCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGa             <  1:1047752/66‑1 (MQ=255)
                                                            tttCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTc        >  1:945801/1‑71 (MQ=255)
                                                            tttCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTc        >  1:1732644/1‑71 (MQ=255)
                                                              tCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGt                       >  1:1815069/1‑54 (MQ=255)
                                                              tCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTc        <  1:1046696/69‑1 (MQ=255)
                                                              tCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTc        <  1:1286797/69‑1 (MQ=255)
                                                              tCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGa      >  1:278775/1‑71 (MQ=255)
                                                              tCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGa      >  1:1327470/1‑71 (MQ=255)
                                                              tCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGa      >  1:1404454/1‑71 (MQ=255)
                                                               cATTCTTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGAc     >  1:1327503/1‑71 (MQ=255)
                                                               cATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGAc     >  1:526274/1‑71 (MQ=255)
                                                                aTTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGAc     <  1:2476698/70‑1 (MQ=255)
                                                                aTTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGAc     <  1:2473573/70‑1 (MQ=255)
                                                                   ccTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATcga                            >  1:2784624/1‑44 (MQ=255)
                                                                   ccTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGTCTTTGACATTCGACTAg  <  1:1792412/70‑1 (MQ=255)
                                                                   ccTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGa      >  1:1409203/1‑66 (MQ=255)
                                                                   ccTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGACTAg  >  1:927307/1‑70 (MQ=255)
                                                                    cTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGACTAg  >  1:328074/1‑69 (MQ=255)
                                                                    cTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGACTAg  >  1:1025215/1‑69 (MQ=255)
                                                                    |                                                                    
GATGGATAAGCTGGATGTGATCCTGCTGATGTCCGTCAACCCTGGTTTCGGCGGTCAGTCTTTCATTCCTCAAACACTGGATAAACTGCGCGAAGTACGTCGCCGTATCGACGAGTCTGGCTTTGACATTCGACTAG  >  W3110S.gb/4125745‑4125881

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