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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,596,127 G→A 29.7% S157S (TCC→TCT)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,596,1270GA29.7% 119.5 / 60.4 88S157S (TCC→TCT) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (31/30);  new base A (12/14);  total (44/44)
Fisher's exact test for biased strand distribution p-value = 8.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCACCATCACCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTA  >  minE/2596057‑2596193
                                                                       |                                                                  
gCACCATCACCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTg                                                                    <  1:3655638/71‑1 (MQ=255)
    cATAACGGAGGCGTACT‑GCGCAAAGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAgaaa                                                                >  1:3207204/1‑69 (MQ=255)
    cATAACGGAGGCGTACT‑GCGCAAAGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAgaaa                                                                >  1:2358490/1‑69 (MQ=255)
    cATAACGGAGGCGTACT‑GCGCAAAGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAgaa                                                                 >  1:4646796/1‑69 (MQ=255)
        aCCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTg                                                                    >  1:467677/1‑63 (MQ=255)
        aCCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACaa                                                             >  1:2641538/1‑70 (MQ=255)
        aCCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAAt                                                            <  1:249723/71‑1 (MQ=255)
        aCCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAAt                                                            <  1:1330378/71‑1 (MQ=255)
          cGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAAt                                                            >  1:3443319/1‑69 (MQ=255)
              gCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCgg                                                      >  1:1004157/1‑71 (MQ=255)
               cGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGc                                                     <  1:4355585/71‑1 (MQ=255)
                  aTTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATa                                                           <  1:1196447/62‑1 (MQ=255)
                   ttCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTg                                                                    >  1:2173524/1‑52 (MQ=255)
                   ttCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTg                                                                    >  1:4434754/1‑52 (MQ=255)
                   ttCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGAAATTCACAAGGTTGGAGACAATAAGCGGCAgg                                                  >  1:2493236/1‑70 (MQ=255)
                    tCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAg                                                         >  1:5291843/1‑62 (MQ=255)
                       cgcaaaGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTgg                                              >  1:3387305/4‑71 (MQ=255)
                       cgcaaaGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTgg                                              >  1:3393996/4‑71 (MQ=255)
                       cg‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGc                                             >  1:1196194/1‑71 (MQ=255)
                       cg‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGc                                             <  1:3513256/71‑1 (MQ=255)
                       cg‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGc                                             >  1:351590/1‑71 (MQ=255)
                       cg‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGc                                             <  1:1877612/71‑1 (MQ=255)
                        g‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCg                                            <  1:3270281/71‑1 (MQ=255)
                         caaaGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAGAAACa                                                              <  1:5531407/52‑1 (MQ=255)
                          aaaGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCgg                                                      <  1:11626/60‑1 (MQ=255)
                          aaaGCTCAGACCGAAGAAGTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCgg                                                      <  1:3444343/60‑1 (MQ=255)
                          aaaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTTGAGACAATAAGCGGCAGGCTGGCgg                                           >  1:2759706/1‑71 (MQ=255)
                            aGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTa                                         >  1:4325507/1‑71 (MQ=255)
                                  ggCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGga                                                                  >  1:3288686/1‑40 (MQ=255)
                                  ggCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGga                                                                  >  1:4091978/1‑40 (MQ=255)
                                  ggCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGga                                                                  >  1:3708164/1‑40 (MQ=255)
                                  ggCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGga                                                                  >  1:4005825/1‑40 (MQ=255)
                                  ggCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGga                                                                  >  1:1260618/1‑40 (MQ=255)
                                  ggCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGga                                                                  >  1:5066925/1‑40 (MQ=255)
                                   gCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTg                                                                    <  1:15690/37‑1 (MQ=255)
                                   gCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATa                                                           <  1:303257/46‑1 (MQ=255)
                                    ccgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCaa                                  <  1:4561973/67‑1 (MQ=255)
                                    ccAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATa                                                           <  1:5329182/45‑1 (MQ=255)
                                    ccAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                 <  1:61551/71‑1 (MQ=255)
                                     cgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAta                                <  1:1027594/69‑2 (MQ=255)
                                     cgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAt                                 >  1:568668/3‑70 (MQ=255)
                                      gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAtaa                               <  1:2907473/70‑3 (MQ=255)
                                      gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAtaa                               <  1:1074104/70‑3 (MQ=255)
                                      aaaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCa                                   <  1:254872/67‑1 (MQ=255)
                                      aaaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGa                               <  1:2147117/71‑1 (MQ=255)
                                       aagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGc                                    <  1:2102362/65‑1 (MQ=255)
                                       aaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGaa                              <  1:1532620/71‑1 (MQ=255)
                                        aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCgg                                                      <  1:2897764/46‑1 (MQ=255)
                                        aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAAt                             >  1:343780/1‑71 (MQ=255)
                                        aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAAt                             >  1:2210402/1‑71 (MQ=255)
                                         gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATa                                                           >  1:627901/1‑40 (MQ=255)
                                         gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATa                                                           >  1:4757351/1‑40 (MQ=255)
                                         gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTgg                                              >  1:5434049/1‑53 (MQ=255)
                                         gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATc                            <  1:1231880/71‑1 (MQ=255)
                                         gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATc                            >  1:8113/1‑71 (MQ=255)
                                         gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATc                            <  1:1474192/71‑1 (MQ=255)
                                            aTCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCgg                         >  1:25208/1‑71 (MQ=255)
                                              cAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                           >  1:3068564/1‑51 (MQ=255)
                                                 aggAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGc                                    <  1:920563/54‑1 (MQ=255)
                                                   gagaCGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAt                  >  1:618636/4‑71 (MQ=255)
                                                   gagaCGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAt                  >  1:5038161/4‑71 (MQ=255)
                                                   gAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                  <  1:332899/71‑1 (MQ=255)
                                                   gAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                  <  1:5361754/71‑1 (MQ=255)
                                                      aCGATATTCACCAGGTTGGAGACAATAAGCGTCAGCCt                                                >  1:1199707/1‑38 (MQ=38)
                                                       cGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACg              <  1:1992297/71‑1 (MQ=255)
                                                       cGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACg              <  1:5620776/71‑1 (MQ=255)
                                                       cGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGAca              <  1:2088555/71‑2 (MQ=255)
                                                        gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGc                                             >  1:580845/1‑39 (MQ=255)
                                                        gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGgccgcc                    <  1:1043670/64‑1 (MQ=255)
                                                        gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGa             <  1:1039141/71‑1 (MQ=255)
                                                        gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGa             <  1:1032259/71‑1 (MQ=255)
                                                         atatTCACCAGGTTGGAGACAATAAGCGGCAGGCTgg                                              >  1:3356018/1‑37 (MQ=255)
                                                           atTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATc                            >  1:2517566/1‑53 (MQ=255)
                                                            ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTAt                                        >  1:1198090/1‑40 (MQ=255)
                                                            ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                 <  1:86279/47‑1 (MQ=255)
                                                            ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                 <  1:5580356/47‑1 (MQ=255)
                                                            ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGc         <  1:2205322/71‑1 (MQ=255)
                                                            ttCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGc         <  1:2890870/71‑1 (MQ=255)
                                                            ttCACCAGCTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAt                  <  1:2379629/62‑1 (MQ=255)
                                                              cACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGcc        <  1:5543577/70‑1 (MQ=255)
                                                              cACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGcc        <  1:4629170/70‑1 (MQ=255)
                                                              cACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGc         >  1:3401340/1‑69 (MQ=255)
                                                              cACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGcc        <  1:2777360/70‑1 (MQ=255)
                                                                 cAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCg    <  1:1548326/71‑1 (MQ=255)
                                                                 cAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtg    >  1:3791224/1‑69 (MQ=255)
                                                                  aGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                  >  1:3866034/1‑56 (MQ=255)
                                                                  aGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                  >  1:3513260/1‑56 (MQ=255)
                                                                  aGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCa       >  1:2594433/1‑67 (MQ=255)
                                                                   ggTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCg    >  1:4563082/1‑69 (MQ=255)
                                                                   ggTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtgtc  >  1:1878442/1‑70 (MQ=255)
                                                                   ggTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtgtc  >  1:2786185/1‑70 (MQ=255)
                                                                    gTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGAcaa             <  1:4699307/59‑3 (MQ=255)
                                                                    gTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtg    <  1:204203/68‑3 (MQ=255)
                                                                       ggAGACAATAAGCGGCAGGCTGGCGGTATCGGaaa                                  >  1:995273/1‑35 (MQ=255)
                                                                       |                                                                  
GCACCATCACCGAGGCGTATTCGCG‑AAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTA  >  minE/2596057‑2596193

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