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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,211,677 C→T 19.0% intergenic (+169/‑26) dnaG → / → rpoD DNA primase/RNA polymerase, sigma 70 (sigma D) factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,211,6770CT19.0% 195.3 / 37.1 84intergenic (+169/‑26)dnaG/rpoDDNA primase/RNA polymerase, sigma 70 (sigma D) factor
Reads supporting (aligned to +/- strand):  ref base C (43/25);  new base T (6/10);  total (49/35)
Fisher's exact test for biased strand distribution p-value = 9.00e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

AAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACC  >  W3110S.gb/3211612‑3211744
                                                                 |                                                                   
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGTGTCAATCGCCCAACACCAACCTCATGa                                                                 >  1:4004438/1‑70 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACTTCATGa                                                                 <  1:41/70‑1 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGa                                                                 >  1:10340/1‑70 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGa                                                                 >  1:2186508/1‑70 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGa                                                                 >  1:103517/1‑70 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGa                                                                 >  1:630460/1‑70 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGa                                                                 >  1:404289/1‑70 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGa                                                                 >  1:2645385/1‑70 (MQ=255)
 aacaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGaaa                                                               >  1:256292/1‑71 (MQ=255)
  acaacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                              <  1:3537912/71‑1 (MQ=255)
   caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAAt                                                              >  1:1122829/1‑70 (MQ=255)
   caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                              >  1:1111623/1‑70 (MQ=255)
   caacCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAAt                                                              >  1:4298343/1‑70 (MQ=255)
     acCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAg                                                           <  1:3434394/71‑1 (MQ=255)
        gTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATg                                                                  <  1:1946055/61‑1 (MQ=255)
         ttGGATTTCAGCGTTAACGGCTGAAGGACATCGTGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                       >  1:2372331/1‑71 (MQ=255)
         ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGtgtg                                                       <  1:623426/71‑1 (MQ=255)
         ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                       >  1:160372/1‑71 (MQ=255)
         ttGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                       <  1:2089523/71‑1 (MQ=255)
          tGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGaa                                                                >  1:3078345/1‑61 (MQ=255)
           ggATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGaaa                                                               >  1:3910011/1‑61 (MQ=255)
           ggATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                     >  1:3759871/1‑71 (MQ=255)
                    cGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCt                                             >  1:2118160/1‑70 (MQ=255)
                     gTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                           <  1:3562721/71‑1 (MQ=255)
                      ttAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTAt                                          <  1:1154904/71‑1 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAgtg                                                         >  1:1777960/1‑54 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAgtg                                                         >  1:2683374/1‑54 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         >  1:3854571/1‑70 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         >  1:3125219/1‑70 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         >  1:1021749/1‑70 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         >  1:1071723/1‑70 (MQ=255)
                        aaCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACAGTCTTATg                                         >  1:1900165/1‑70 (MQ=255)
                         aCGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         >  1:4102107/1‑69 (MQ=255)
                            gCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGaa                                                                >  1:1277471/1‑43 (MQ=255)
                               gAAGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGtgtg                                                       <  1:3301776/49‑1 (MQ=255)
                               gAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa                                 >  1:2500399/1‑71 (MQ=255)
                                aaGGACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGtgtg                                                       <  1:3980064/48‑1 (MQ=255)
                                aaGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc                                >  1:4525229/1‑71 (MQ=255)
                                 aGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATaa                                                            >  1:180514/1‑42 (MQ=255)
                                  ggACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAccc                              <  1:3628485/71‑1 (MQ=255)
                                  ggACATCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAccc                              <  1:2156505/71‑1 (MQ=255)
                                     cATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGAt                                                    <  1:3775847/46‑1 (MQ=255)
                                       tCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTTTGGATACCGTCt                                             <  1:4533987/51‑1 (MQ=255)
                                       tCGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCt                                             <  1:4539491/51‑1 (MQ=255)
                                        cGGGTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATAc                                                  >  1:3746052/1‑45 (MQ=255)
                                        cGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATgg                                        >  1:2854469/1‑55 (MQ=255)
                                         gggTCAATCGCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca                       >  1:3764437/1‑71 (MQ=255)
                                         gggTCAATCGCCCAACACCAACCTCATGAAATAAGtgtg                                                       <  1:2912551/39‑1 (MQ=255)
                                         gggTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGa                                                     >  1:3726855/1‑41 (MQ=255)
                                         gggTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTc                        <  1:2642218/70‑1 (MQ=255)
                                           gTCAATCGCCCAACACCAACCTTTTGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca                     <  1:4406729/71‑1 (MQ=255)
                                           gTCAATCGCCCAACACCAACCTCATGAAATAAGTGTgg                                                      >  1:2156874/1‑38 (MQ=255)
                                           gTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca                     <  1:3713253/71‑1 (MQ=255)
                                            tCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca                     <  1:2740273/70‑1 (MQ=255)
                                               aTCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc                                >  1:920734/1‑56 (MQ=255)
                                               aTCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc                                >  1:3703639/1‑56 (MQ=255)
                                                tCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         <  1:4649443/46‑1 (MQ=255)
                                                  gCCCAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa              >  1:2138351/1‑71 (MQ=255)
                                                  gCCCAACACCAACCTCATGAAATAAGTGTGTATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaa               <  1:1004460/70‑1 (MQ=255)
                                                  gCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa              >  1:446826/1‑71 (MQ=255)
                                                  gCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa              >  1:1681160/1‑71 (MQ=255)
                                                     cAACACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca                     <  1:531864/61‑1 (MQ=255)
                                                      aaCACCAACCTTATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGa                <  1:1527347/65‑1 (MQ=255)
                                                      aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtc          <  1:2648076/71‑1 (MQ=255)
                                                      aaCACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtc          <  1:622215/71‑1 (MQ=255)
                                                       acacCAACCTCATGAAATAAGTGTGGATACCGTCtt                                            <  1:2849961/36‑1 (MQ=255)
                                                       acacCAACCTCATGAAATAAGTGTGGATACCGTCt                                             <  1:1463787/35‑1 (MQ=255)
                                                       acacCAACCTCATGAAATAAGTGTGGATACCGTCt                                             <  1:229674/35‑1 (MQ=255)
                                                       acacCAACCTCATGAAATAAGTGTGGATACCGTCTTa                                           <  1:4606669/37‑1 (MQ=255)
                                                       acacCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAAct            <  1:2372523/68‑1 (MQ=255)
                                                        cacCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAActtctt        >  1:560630/1‑71 (MQ=255)
                                                         acCAACCTCATGAAATAAGTGTGGATACCGTCTTATg                                         >  1:4631932/1‑37 (MQ=255)
                                                         acCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc                                >  1:1258450/1‑46 (MQ=255)
                                                         acCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTg       >  1:2041155/1‑71 (MQ=255)
                                                          ccAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGt      >  1:4010102/1‑71 (MQ=255)
                                                            aaCCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCa    >  1:1775415/1‑71 (MQ=255)
                                                            aaCCTCATGAAATAAGTGTGGATACAGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCa    >  1:828551/1‑71 (MQ=255)
                                                              ccTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaa                                  <  1:2502407/39‑1 (MQ=255)
                                                              ccTCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaa                                  <  1:564980/39‑1 (MQ=255)
                                                              ccTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCt                  <  1:2537905/55‑1 (MQ=255)
                                                              ccTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCAcc  >  1:3130797/1‑71 (MQ=255)
                                                                tCATGAAATAAGTGTGGATACCGTCTTATGGAGCaaaa                                 >  1:1445521/1‑38 (MQ=255)
                                                                tCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc                                <  1:167637/39‑1 (MQ=255)
                                                                tCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGa                >  1:3011743/1‑55 (MQ=255)
                                                                 cATCAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTCaaa              >  1:3086267/1‑56 (MQ=255)
                                                                 |                                                                   
AAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACC  >  W3110S.gb/3211612‑3211744

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