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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,806,473 G→A 35.4% P198P (CCG→CCA)  yicI → predicted alpha‑glucosidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,806,4730GA35.4% 70.8 / 62.9 65P198P (CCG→CCA) yicIpredicted alpha‑glucosidase
Reads supporting (aligned to +/- strand):  ref base G (22/20);  new base A (12/11);  total (34/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

ATGGCCAGACGGTAGAGACCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGAAGTGG  >  W3110S.gb/3806403‑3806540
                                                                      |                                                                   
aTGGCCAGACGGTAGAGACCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCg                                                                     >  1:3948251/1‑71 (MQ=255)
   gCCAGACGGTAGAGACCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCATTc                                                                  <  1:4975222/71‑1 (MQ=255)
            tAGAGACCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGa                                                           >  1:273062/1‑69 (MQ=255)
            tAGAGACCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACt                                                         <  1:210408/71‑1 (MQ=255)
               agaCCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAAc                                                      <  1:1621763/71‑1 (MQ=255)
                 aCCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCg                                                    >  1:5135912/1‑71 (MQ=255)
                   cTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGt                                                   <  1:390461/70‑1 (MQ=255)
                      gAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCg                                                    <  1:2870295/66‑1 (MQ=255)
                      gAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGt                                                <  1:354195/70‑1 (MQ=255)
                      gAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGt                                                >  1:3458850/1‑70 (MQ=255)
                         ccGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTGGTTATg                                            <  1:4040327/71‑1 (MQ=255)
                          cGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATgg                                           <  1:2186351/71‑1 (MQ=255)
                          cGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATgg                                           <  1:3710193/71‑1 (MQ=255)
                           gggACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGT‑‑TACATGACTAACCGTGGTTa                                              >  1:3231538/1‑65 (MQ=255)
                            ggACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTgg                                                 <  1:291736/63‑1 (MQ=255)
                            ggACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTgg                                                 <  1:2108997/63‑1 (MQ=255)
                              aCGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTAt                                             >  1:2537105/1‑65 (MQ=255)
                               cggcggCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTAc                                      <  1:115499/71‑1 (MQ=255)
                                ggcggcACAAGTACTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTgg                                                 <  1:2546592/59‑1 (MQ=255)
                                     cacaAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATggg                                          >  1:2171082/1‑61 (MQ=255)
                                     cacaAGTACTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTc                                 >  1:2262370/1‑70 (MQ=255)
                                         aGTACTGAACAGGCGTATAAAAATATCCCGTTCTACa                                                              >  1:2040694/1‑37 (MQ=255)
                                          gTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTa                                              >  1:2832984/1‑52 (MQ=255)
                                             cTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATccc                        >  1:1331092/1‑71 (MQ=255)
                                             cTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATcc                         <  1:1444472/70‑1 (MQ=255)
                                             cTGAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatca                            >  1:2830165/1‑67 (MQ=255)
                                               gAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATccc                        >  1:4282163/1‑69 (MQ=255)
                                               gAACAGGCGTATAAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATccc                        >  1:1380932/1‑69 (MQ=255)
                                                aaCAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAg                     >  1:1487007/1‑71 (MQ=255)
                                                  cAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatca                            >  1:3636316/1‑62 (MQ=255)
                                                      cGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAgtg                   >  1:3975530/1‑67 (MQ=255)
                                                        tataAAAATATCCCGTTCTACATGACTAACCGTGGt                                                <  1:2232354/36‑1 (MQ=255)
                                                        tataAAAATATCCCGTTCTACATGACTAACCGTGGTTATgg                                           <  1:1622285/41‑1 (MQ=255)
                                                        tataAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatc                             <  1:4650590/55‑1 (MQ=255)
                                                        tataAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatc                             <  1:3499814/55‑1 (MQ=255)
                                                        tataAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATccc                        <  1:1215212/60‑1 (MQ=255)
                                                          taAAAATATCCCGTTCTACATGACTAACCGTGGTTAt                                             <  1:356402/37‑1 (MQ=255)
                                                          taAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtt           >  1:1355750/1‑71 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATggg                                          >  1:3566825/1‑40 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATggg                                          >  1:2553864/1‑40 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTAc                                      >  1:3252852/1‑44 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatca                            >  1:3324824/1‑54 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTctct            <  1:2421446/70‑1 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtt           <  1:4288921/71‑1 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtt           <  1:2676080/71‑1 (MQ=255)
                                                          taAAAATATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtt           <  1:4027480/71‑1 (MQ=255)
                                                            aaaaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCa                      >  1:807211/1‑58 (MQ=255)
                                                            aaaaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGtc               <  1:3442298/65‑1 (MQ=255)
                                                            aaaaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGtc               <  1:2267130/65‑1 (MQ=255)
                                                            aaaaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtttt         >  1:2309711/1‑71 (MQ=255)
                                                            aaaaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtttt         >  1:1184936/1‑71 (MQ=255)
                                                            aaaaTATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatcat                           >  1:4506607/1‑53 (MQ=255)
                                                            aaaaTATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatcat                           >  1:46553/1‑53 (MQ=255)
                                                            aaaaTATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatcat                           >  1:5106277/1‑53 (MQ=255)
                                                            aaaaTATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatcat                           >  1:3471777/1‑53 (MQ=255)
                                                            aaaaTATCCCATTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCtt           <  1:1475942/69‑1 (MQ=255)
                                                             aaaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAgtg                   >  1:129895/1‑60 (MQ=255)
                                                              aaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTg        <  1:5037662/70‑1 (MQ=255)
                                                              aaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGa       <  1:996157/71‑1 (MQ=255)
                                                              aaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGa       <  1:821623/71‑1 (MQ=255)
                                                              aaTATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGa       <  1:1122978/71‑1 (MQ=255)
                                                                  tCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatc                             >  1:4921650/1‑45 (MQ=255)
                                                                  tCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatc                             >  1:814514/1‑45 (MQ=255)
                                                                  tCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAatc                             >  1:1539815/1‑45 (MQ=255)
                                                                   cccGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGAAGTgg  >  1:4505054/1‑71 (MQ=255)
                                                                   cccGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGAAGTgg  >  1:4242803/1‑71 (MQ=255)
                                                                      |                                                                   
ATGGCCAGACGGTAGAGACCTGGAACCGGGACGGCGGCACAAGTACTGAACAGGCGTATAAAAATATCCCGTTCTACATGACTAACCGTGGTTATGGGGTACTGGTCAATCATCCCCAGTGTGTCTCTTTTGAAGTGG  >  W3110S.gb/3806403‑3806540

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