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 4,094,617 G→A 16.4% L60L (CTG→TTG)  gntY ← predicted gluconate transport associated protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,094,6170GA16.4% 185.4 / 25.1 73L60L (CTG→TTG) gntYpredicted gluconate transport associated protein
Reads supporting (aligned to +/- strand):  ref base G (29/32);  new base A (8/4);  total (37/36)
Fisher's exact test for biased strand distribution p-value = 3.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01

CGGTAACAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCCACATTCAGCG  >  W3110S.gb/4094548‑4094687
                                                                     |                                                                      
cGGTAACAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTcagcag                                                                        >  1:2411703/1‑70 (MQ=255)
 ggTAACAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGt                                                                      >  1:3993556/1‑71 (MQ=255)
   tAACAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCa                                                                    <  1:516129/71‑1 (MQ=255)
    aaCAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTc                                                                     >  1:2004392/1‑69 (MQ=255)
    aaCAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCa                                                                    >  1:3235064/1‑70 (MQ=255)
    aaCAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCa                                                                    <  1:2689481/70‑1 (MQ=255)
     aCAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCaaa                                                                  >  1:3633292/1‑71 (MQ=255)
     aCAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCaa                                                                   <  1:1487752/70‑1 (MQ=255)
     aCAAAATCGATCTCTGCATCTTCCAGGTAGGGTGCGCTTCACTCATCAACCTACGCGGTCAGCAGGTCaa                                                                   <  1:3306471/70‑1 (MQ=255)
        aaaTCGATCTCTGCATCTTCCAGGTATGGTGCTCTTAACTCATCAACATACGCGGTCAGCAGGTCAAAtt                                                                >  1:3569392/1‑70 (MQ=255)
        aaaTCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAAttt                                                               <  1:2376997/71‑1 (MQ=255)
         aaTCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAAt                                                                 >  1:1096719/1‑68 (MQ=255)
         aaTCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTc                                                              <  1:3260630/71‑1 (MQ=255)
          aTCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCa                                                             <  1:1259934/71‑1 (MQ=255)
           tCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAg                                                            <  1:1854803/71‑1 (MQ=255)
             gATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAAGTCAAATTTCAtgg                                                          >  1:2109419/1‑71 (MQ=255)
               tctcTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCaa                                                                   >  1:2488825/1‑60 (MQ=255)
               tctcTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCt                                                        >  1:2529937/1‑71 (MQ=255)
               tctcTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCt                                                        >  1:3921745/1‑71 (MQ=255)
               tctcTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCt                                                        >  1:3264771/1‑71 (MQ=255)
                   tGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCtgt                                                      <  1:942121/69‑1 (MQ=255)
                   tGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCt                                                        <  1:1386728/67‑1 (MQ=255)
                   tGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCTgtgt                                                    >  1:2540125/1‑71 (MQ=255)
                     cagcTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCg                                                  <  1:1673099/68‑1 (MQ=255)
                     cATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTgtgt                                                    <  1:902241/69‑1 (MQ=255)
                     cATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCg                                                  >  1:3915185/1‑71 (MQ=255)
                     cATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCg                                                  >  1:3342390/1‑71 (MQ=255)
                     cATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCTgtgt                                                    <  1:3291294/69‑1 (MQ=255)
                           ccAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCt                                            >  1:4154102/1‑71 (MQ=255)
                           ccAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCt                                            >  1:2963232/1‑71 (MQ=255)
                             aGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTc                                          <  1:3797396/71‑1 (MQ=255)
                             aGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCtt                                           >  1:4477042/1‑70 (MQ=255)
                               gTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCg                                                  <  1:2470476/61‑1 (MQ=255)
                                 aTGGTGCGCTTAACTCATCAACATACGCGGTCAGCAgg                                                                       <  1:2448570/38‑1 (MQ=255)
                                 aTGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAg                                                            >  1:2018496/1‑49 (MQ=255)
                                  tGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCcaca                                      <  1:1870898/70‑1 (MQ=255)
                                  tGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCcaca                                      <  1:2683683/70‑1 (MQ=255)
                                  tGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCcaca                                      <  1:716670/70‑1 (MQ=255)
                                  tGGTGCGCTTAACTCATCAACATACG‑GGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGc                                    >  1:3687526/1‑71 (MQ=255)
                                    gTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCgg                                                 >  1:3114809/1‑57 (MQ=255)
                                    gTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCg                                   >  1:151660/1‑71 (MQ=255)
                                     tGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCATAttt                                                               <  1:626939/42‑1 (MQ=255)
                                     tGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCg                                                  <  1:212967/55‑1 (MQ=255)
                                     tGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGt                                  <  1:119563/71‑1 (MQ=255)
                                     tGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGt                                  <  1:1868913/71‑1 (MQ=255)
                                      gcgcTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCgg                                                 >  1:3353987/1‑55 (MQ=255)
                                      gcgcTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCgg                                                 >  1:4017764/1‑55 (MQ=255)
                                       cgcTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCg                                                  <  1:365653/53‑1 (MQ=255)
                                         cTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCt                                                        >  1:1816131/1‑45 (MQ=255)
                                         cTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCcgg                              >  1:564545/1‑71 (MQ=255)
                                         cTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCcgg                              <  1:3824687/71‑1 (MQ=255)
                                          ttAACTCATCAACATACGCGGTCAGCAGGTCAAAttt                                                               <  1:1334716/37‑1 (MQ=255)
                                          ttAACTCATCAACATACGCGGTCAGCAGGTCAAAt                                                                 <  1:1024238/35‑1 (MQ=255)
                                            aaCTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCcggcg                            >  1:2744645/1‑70 (MQ=255)
                                            aaCTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCcggc                             >  1:2975073/1‑69 (MQ=255)
                                            aaCTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTc                                 >  1:4598888/1‑65 (MQ=255)
                                             aCTCATCAACATACGCGGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCcggcgg                           <  1:1091180/70‑1 (MQ=255)
                                              cTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGAc                         <  1:707617/71‑1 (MQ=255)
                                                 atcaACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACaa                       >  1:3372213/1‑70 (MQ=255)
                                                 atcaACATACGCGGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAAt                      <  1:3153495/71‑1 (MQ=255)
                                                  tcaACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATa                     <  1:2092825/71‑1 (MQ=255)
                                                   caACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCcggcg                            <  1:4315612/63‑1 (MQ=255)
                                                   caACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAAt                      >  1:3438068/1‑69 (MQ=255)
                                                   caACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAAt                      >  1:1151284/1‑69 (MQ=255)
                                                     aCATACGCGGTCAGCAGGTCAAATTTCAGGGCtgt                                                      <  1:3946397/35‑1 (MQ=255)
                                                     aCATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAg                   >  1:3497831/1‑70 (MQ=255)
                                                     aCATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGa                  <  1:2609678/71‑1 (MQ=255)
                                                     aCATACGCGGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGt                                                >  1:3634577/1‑41 (MQ=255)
                                                       aTACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGaaa                >  1:1968312/1‑71 (MQ=255)
                                                        tACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAAc               <  1:1724106/71‑1 (MQ=255)
                                                         aCGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACg              >  1:4330081/1‑71 (MQ=255)
                                                          cgcgGTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGaa                 <  1:1142294/67‑1 (MQ=255)
                                                             ggTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGa                  >  1:546787/1‑63 (MQ=255)
                                                             ggTCAGCAAGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCca           >  1:552077/1‑70 (MQ=255)
                                                              gTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCcaca         <  1:4491655/71‑1 (MQ=255)
                                                                cagcagGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCCACAtt       >  1:227367/1‑71 (MQ=255)
                                                                   cagGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCCACATTCAg    >  1:428852/1‑71 (MQ=255)
                                                                     ggTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCCACATTCAGCg  <  1:2988328/71‑1 (MQ=255)
                                                                     ggTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCCACATTCAGCg  >  1:1057380/1‑71 (MQ=255)
                                                                     |                                                                      
CGGTAACAAAATCGATCTCTGCATCTTCCAGGTATGGTGCGCTTAACTCATCAACATACGCGGTCAGCAGGTCAAATTTCAGGGCTGTGTCGGTGGCTTCCACAGCGTCCGGCGGACAATAAGAAACGCCACATTCAGCG  >  W3110S.gb/4094548‑4094687

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