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 4,527,342 C→T 10.6% E479K (GAG→AAG)  yjhG ← predicted dehydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,527,3420CT10.6% 195.4 / 11.0 66E479K (GAG→AAG) yjhGpredicted dehydratase
Reads supporting (aligned to +/- strand):  ref base C (27/32);  new base T (4/3);  total (31/35)
Fisher's exact test for biased strand distribution p-value = 6.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGT  >  W3110S.gb/4527273‑4527407
                                                                     |                                                                 
cGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCg                                                                  <  1:1859714/71‑1 (MQ=255)
  ccAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGa                                                                >  1:2681639/1‑71 (MQ=255)
        atGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGAt                                                           >  1:768008/1‑70 (MQ=255)
         tGACCAGAATATCGCGCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATaa                                                         <  1:2198582/71‑1 (MQ=255)
         tGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTTGGACAGATaa                                                         <  1:1493623/71‑1 (MQ=255)
         tGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTTGGACAGATaa                                                         <  1:705012/71‑1 (MQ=255)
         tGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATaa                                                         <  1:720599/71‑1 (MQ=255)
          gACCAGGATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATaaa                                                        >  1:358674/1‑71 (MQ=255)
            ccAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTTGGACAGATAAAcc                                                      <  1:2345677/71‑1 (MQ=255)
             cAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCt                                                     <  1:1877081/71‑1 (MQ=255)
             cAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCt                                                     <  1:1071821/71‑1 (MQ=255)
               gAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTc                                                   <  1:1659207/71‑1 (MQ=255)
                  tatCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGc                                                 >  1:2347002/1‑70 (MQ=255)
                    tCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGa                                                            >  1:1397235/1‑57 (MQ=255)
                    tCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTTGCca                                               >  1:2201155/1‑70 (MQ=255)
                         cgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                         <  1:721425/71‑1 (MQ=255)
                         cgccTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                         >  1:1501943/1‑71 (MQ=255)
                           ccTTGATCTTGTCATCTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTa                                       <  1:2628547/71‑1 (MQ=255)
                             ttGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                         <  1:1977144/67‑1 (MQ=255)
                               gATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCca                                               >  1:19862/1‑59 (MQ=255)
                                aTCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACGTTCGCCACACCTTTATGGt                                   <  1:1379088/70‑1 (MQ=255)
                                   ttGTCATGTTTGATATCGTAAATCGCACTTTTCTTGGACAGATAAACCTTCGCCACACCTTTATGGTaa                                 >  1:2262426/1‑69 (MQ=255)
                                     gTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTc                                                   <  1:2547855/49‑1 (MQ=255)
                                     gTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATa                               <  1:950944/69‑1 (MQ=255)
                                      tCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGt                                   <  1:2717285/64‑1 (MQ=255)
                                        aTGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                         <  1:608975/56‑1 (MQ=255)
                                        aTGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCtt                                         <  1:1059519/56‑1 (MQ=255)
                                        aTGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATa                           <  1:2775713/70‑1 (MQ=255)
                                          gTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                            >  1:1192401/1‑67 (MQ=255)
                                          gTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                            >  1:1552583/1‑67 (MQ=255)
                                           tttGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCtt                       >  1:331803/1‑71 (MQ=255)
                                           tttGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCtt                       <  1:952087/71‑1 (MQ=255)
                                           tttGATATAGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATg                                     >  1:1833994/1‑57 (MQ=255)
                                             tGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTg                      <  1:120487/70‑1 (MQ=255)
                                             tGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTg                      <  1:2656112/70‑1 (MQ=255)
                                             tGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTg                      <  1:279059/70‑1 (MQ=255)
                                             tGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGc                     >  1:1177195/1‑71 (MQ=255)
                                             tGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGc                     >  1:191636/1‑71 (MQ=255)
                                              gATATCGTAAATCGCACTTTTCTTGGACAGATAAACCTTCGCCACACCTTTa                                       >  1:1763756/1‑52 (MQ=255)
                                                  tCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATa                               <  1:1302416/56‑1 (MQ=255)
                                                  tCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                            <  1:285254/59‑1 (MQ=255)
                                                    gTAAATCGCACTTTTCTTGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaa              >  1:2594508/1‑71 (MQ=255)
                                                    gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGc                                                 <  1:75903/36‑1 (MQ=255)
                                                    gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCca                                               >  1:2501994/1‑38 (MQ=255)
                                                    gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATAc                          >  1:576673/1‑59 (MQ=255)
                                                    gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCtca                  >  1:628336/1‑67 (MQ=255)
                                                    gTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaa              >  1:1063122/1‑71 (MQ=255)
                                                       aaTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaatca           <  1:1793746/71‑1 (MQ=255)
                                                       aaTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaatca           >  1:1480693/1‑71 (MQ=255)
                                                       aaTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaatc            <  1:631848/70‑1 (MQ=255)
                                                        aTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTa                                       <  1:2485373/42‑1 (MQ=255)
                                                        aTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTa                                       <  1:2254291/42‑1 (MQ=255)
                                                        aTCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTa                                       <  1:1443145/42‑1 (MQ=255)
                                                         tCGCAATTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCtc                   >  1:157235/1‑61 (MQ=255)
                                                           gCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGAt                            <  1:844839/50‑1 (MQ=255)
                                                           gCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCg        <  1:1097364/70‑1 (MQ=255)
                                                            cACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAatcatc         <  1:1147328/68‑1 (MQ=255)
                                                               ttttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCtca                  <  1:985749/56‑1 (MQ=255)
                                                                tttCTTGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGt  >  1:2080866/1‑71 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTaa                                 >  1:1441682/1‑39 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTaa                                 >  1:782070/1‑39 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaa              >  1:759723/1‑58 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaa              >  1:548322/1‑58 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCatcaa              >  1:384641/1‑58 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGt  >  1:1804306/1‑70 (MQ=255)
                                                                 ttCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGt  >  1:898916/1‑70 (MQ=255)
                                                                     |                                                                 
CGCCAATAATGACCAGAATATCGCCCGCCTTGATCTTGTCATGTTTGATATCGTAAATCGCACTTTTCTCGGACAGATAAACCTTCGCCACACCTTTATGGTAATAGATACCTTGCTCATCAATCATCGAGGGGT  >  W3110S.gb/4527273‑4527407

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