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 F8 I0 R2 422 46.8 3726540 94.7% 3529033 61.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 579,794 A→G 59.3% intergenic (+485/‑263) ybcW → / → nohB hypothetical protein/DNA packaging protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb579,7940AG59.3% 54.7 / 101.6 86intergenic (+485/‑263)ybcW/nohBhypothetical protein/DNA packaging protein
Reads supporting (aligned to +/- strand):  ref base A (25/10);  new base G (24/27);  total (49/37)
Fisher's exact test for biased strand distribution p-value = 2.88e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.18e-01

CAGATCAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATCC  >  W3110S.gb/579735‑579856
                                                           |                                                              
cAGATCAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGtt                                                      <  1:2077588/70‑1 (MQ=255)
cAGATCAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGtt                                                      <  1:435968/70‑1 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGa                                                              >  1:1585693/1‑57 (MQ=16)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGAc                                                 >  1:2351781/1‑70 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:3047865/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:2331934/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:1721527/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:1709422/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:3650716/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:1224467/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:3551934/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACa                                                >  1:216429/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACa                                                >  1:2137968/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACa                                                >  1:3470900/1‑71 (MQ=255)
     cAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACa                                                >  1:1874909/1‑71 (MQ=255)
      aaTTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACAt                                               >  1:2672329/1‑71 (MQ=255)
      aaTTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACAt                                               >  1:3684806/1‑71 (MQ=255)
        ttAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGt                                                       <  1:2281066/61‑1 (MQ=255)
         tAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATg                                              >  1:1267355/1‑69 (MQ=255)
          aaTACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATg                                              >  1:204283/1‑68 (MQ=255)
          aaTACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATg                                              >  1:751914/1‑68 (MQ=255)
          aaTACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATg                                              >  1:2527007/1‑68 (MQ=255)
          aaTACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATg                                              >  1:2144828/1‑68 (MQ=255)
            tACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTtgt                                                    <  1:170681/60‑1 (MQ=255)
            tACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTtgt                                                    <  1:3661239/60‑1 (MQ=255)
            tACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTtgt                                                    <  1:93672/60‑1 (MQ=255)
              cGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGa                                                  >  1:2690246/1‑60 (MQ=255)
              cGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAgatg                                        <  1:1150934/70‑1 (MQ=255)
               gATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAgatgat                                      <  1:3119821/71‑1 (MQ=255)
               gATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAgatgat                                      <  1:2240314/71‑1 (MQ=255)
               gATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAgatgat                                      <  1:1304114/71‑1 (MQ=255)
               gATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAgatgat                                      <  1:3552586/71‑1 (MQ=255)
               gATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAgatgat                                      <  1:83100/71‑1 (MQ=255)
                   ccTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAat                                   >  1:3286190/1‑70 (MQ=255)
                   ccTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCAAGTTGTGACATGTAGATGATAat                                   >  1:1966636/1‑70 (MQ=255)
                    cTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAgatgat                                      <  1:2786955/66‑1 (MQ=255)
                     tGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACa                                                >  1:2845344/1‑55 (MQ=255)
                      gCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATaa                                    >  1:3070644/1‑66 (MQ=255)
                         tCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTa                                            <  1:2650673/55‑1 (MQ=255)
                         tCATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTa                                            <  1:2922438/55‑1 (MQ=255)
                         tCATAATTGATTATTTGACGTGGTTT‑ATGGCGTGGATGCACGTTGTGACATGTa                                            <  1:1586457/54‑1 (MQ=18)
                          cATAATTGATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCa                           >  1:2375910/1‑71 (MQ=255)
                             aaTTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATc                            >  1:3060392/1‑67 (MQ=255)
                              aTTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAga                                          >  1:606365/1‑52 (MQ=255)
                              aTTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAga                                          >  1:92932/1‑52 (MQ=255)
                              aTTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAga                                          >  1:2909994/1‑52 (MQ=255)
                              aTTGATTATTTGACGTGGTTTGATGGCGTAGATGAACGTTGTGACATGTAga                                          >  1:1037990/1‑52 (MQ=255)
                                 gATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTtgt                     <  1:688590/70‑1 (MQ=255)
                                 gATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTtgt                     <  1:1370272/70‑1 (MQ=255)
                                 gATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTtgt                     <  1:938555/70‑1 (MQ=255)
                                 gATTATTTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTtgt                     <  1:806146/70‑1 (MQ=255)
                                   ttattTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTggg                  <  1:3558415/71‑1 (MQ=255)
                                   ttattTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTggg                  <  1:30996/71‑1 (MQ=255)
                                     attTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAattat                                >  1:3461994/1‑55 (MQ=255)
                                     attTGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTc                >  1:3352680/1‑71 (MQ=255)
                                     attTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGt                 <  1:2359876/70‑1 (MQ=255)
                                     attTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGt                 <  1:3128326/70‑1 (MQ=255)
                                     attTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTATGTGGGt                 <  1:1664102/70‑1 (MQ=255)
                                      tttGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTc                <  1:993995/70‑1 (MQ=255)
                                      tttGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTc                <  1:3611783/70‑1 (MQ=255)
                                      tttGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTc                <  1:1754732/70‑1 (MQ=255)
                                      tttGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTc                <  1:232608/70‑1 (MQ=255)
                                      tttGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTc                <  1:2507367/70‑1 (MQ=255)
                                        tGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCtt             >  1:2361387/1‑71 (MQ=255)
                                        tGACGTGGTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCtt             >  1:2548959/1‑71 (MQ=255)
                                         gACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCtt             <  1:1573360/70‑1 (MQ=255)
                                         gACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCtt             <  1:2575549/70‑1 (MQ=255)
                                          aCGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCtt             <  1:3169425/69‑1 (MQ=255)
                                              ggTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGc       >  1:3173453/1‑71 (MQ=255)
                                               gTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAat                                   >  1:1506860/1‑42 (MQ=255)
                                               gTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAat                                   >  1:3158445/1‑42 (MQ=255)
                                               gTTTGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGc       >  1:1926199/1‑70 (MQ=255)
                                               gTTTGATGGCGTAGATGCACGTTGTGACATGTAga                                          >  1:2885825/1‑35 (MQ=255)
                                               gTTTGATGGCGTAGATGCACGTTGTGACATGTAga                                          >  1:1476861/1‑35 (MQ=255)
                                               gTTTGATGGCGTAGATGCACGTTGTGACATGTAga                                          >  1:3192136/1‑35 (MQ=255)
                                                tttGATGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGa     <  1:3050409/71‑1 (MQ=255)
                                                 ttGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGAt    >  1:642885/1‑71 (MQ=255)
                                                    aTGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCTATcc  <  1:2718834/70‑1 (MQ=255)
                                                    aTGGCGTGGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATcc  <  1:2954232/70‑1 (MQ=255)
                                                       gCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTtg                      >  1:2715620/1‑47 (MQ=255)
                                                       gCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTtg                      >  1:967556/1‑47 (MQ=255)
                                                         gTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATc   >  1:1190885/1‑64 (MQ=255)
                                                         gTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATc   >  1:1958161/1‑64 (MQ=255)
                                                         gTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATc   >  1:3015910/1‑64 (MQ=255)
                                                         gTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATc   >  1:2560719/1‑64 (MQ=255)
                                                          tAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATcc  <  1:2244538/64‑1 (MQ=255)
                                                           |                                                              
CAGATCAATTAATACGATACCTGCGTCATAATTGATTATTTGACGTGGTTTGATGGCGTAGATGCACGTTGTGACATGTAGATGATAATTATTATCATTTTGTGGGTCCTTTCCGGCGATCC  >  W3110S.gb/579735‑579856

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A