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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,595,380 C→G 20.5% G406G (GGG→GGC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,3800CG20.5% 173.6 / 36.2 83G406G (GGG→GGC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base C (35/31);  new base G (14/3);  total (49/34)
Fisher's exact test for biased strand distribution p-value = 5.06e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCAGAGTAGC  >  minE/2595311‑2595449
                                                                     |                                                                     
cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                                                      <  1:2732030/71‑1 (MQ=255)
cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                                                      >  1:3770257/1‑71 (MQ=255)
cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATc                                                                       <  1:1120769/70‑1 (MQ=255)
cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATc                                                                       <  1:2117169/70‑1 (MQ=255)
   aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                                   <  1:743724/71‑1 (MQ=255)
   aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                                   <  1:3201099/71‑1 (MQ=255)
   aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                                   >  1:3918337/1‑71 (MQ=255)
    gTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATgccgg                                                                   >  1:2285033/1‑68 (MQ=255)
       aaaGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTAc                                                                <  1:483706/70‑1 (MQ=255)
        aaGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACgg                                                              <  1:3658085/71‑1 (MQ=255)
        aaGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACg                                                               >  1:959590/1‑70 (MQ=255)
         agagagACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                                                                   <  1:3873682/65‑1 (MQ=255)
         agagagACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACgg                                                              >  1:3161442/1‑70 (MQ=255)
         agagagACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGa                                                             <  1:2954813/71‑1 (MQ=255)
          gagagaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACgg                                                              >  1:2398976/1‑69 (MQ=255)
            gagaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGt                                                          <  1:743734/71‑1 (MQ=255)
             agaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTa                                                         <  1:1478869/71‑1 (MQ=255)
             agaCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTa                                                         <  1:3810850/71‑1 (MQ=255)
               aCGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAat                                                       <  1:274209/71‑1 (MQ=255)
                cGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAat                                                       <  1:3560902/70‑1 (MQ=255)
                 gTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAatat                                                     >  1:2573543/1‑71 (MQ=255)
                 gTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAatat                                                     <  1:43544/71‑1 (MQ=255)
                 gTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAatat                                                     >  1:1452255/1‑71 (MQ=255)
                  tAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCt                                                                    <  1:2627965/55‑1 (MQ=255)
                  tAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATc                                                    >  1:3292052/1‑71 (MQ=255)
                    gcgcCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATccc                                                  >  1:1454587/1‑71 (MQ=255)
                      gcCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATccc                                                  >  1:1856021/1‑69 (MQ=255)
                       ccAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                                                      <  1:1844456/48‑1 (MQ=255)
                        cAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCaag                                              >  1:3491374/1‑69 (MQ=255)
                        cAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTaa                                                        >  1:1749108/1‑61 (MQ=255)
                        cAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGc                                              >  1:206664/1‑71 (MQ=255)
                         cgcgcGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTa                                                         >  1:114326/2‑59 (MQ=255)
                         aGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCt                                             <  1:609362/71‑1 (MQ=255)
                          gcgcGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCaagt                                             >  1:3247024/1‑67 (MQ=255)
                          gcgcGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCaagt                                             >  1:2844051/1‑67 (MQ=255)
                           cgcAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGa                                           >  1:681841/1‑71 (MQ=255)
                             cggccagaGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGAtt                                         >  1:2394515/3‑70 (MQ=255)
                             cagccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATa                                         <  1:1171195/71‑1 (MQ=255)
                              ggccagaGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGAttg                                        >  1:1393225/2‑69 (MQ=255)
                              agccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAg                                        >  1:1978763/1‑71 (MQ=255)
                               gccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGt                                       >  1:163676/1‑71 (MQ=255)
                               gccagaGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGt                                       <  1:2919751/71‑1 (MQ=255)
                                ccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGa                                           <  1:3816696/66‑1 (MQ=255)
                                 cagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGaa                                                            <  1:3788270/48‑1 (MQ=255)
                                 cagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCa                                     >  1:1325139/1‑71 (MQ=255)
                                  agcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAata                                                      >  1:3429149/1‑53 (MQ=255)
                                    cGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAatat                                                     >  1:3780660/1‑52 (MQ=255)
                                        acaAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAttttt                              >  1:1836209/1‑71 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGaa                                                            >  1:774322/1‑41 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGaa                                                            >  1:2052139/1‑41 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATccc                                                  >  1:2133865/1‑51 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATcc                                                   <  1:2022787/50‑1 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATcc                                                   <  1:636647/50‑1 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATa                                         <  1:1452662/60‑1 (MQ=255)
                                        acaAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCata                                   >  1:468464/1‑66 (MQ=255)
                                         caAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAtttttc                             >  1:110598/1‑71 (MQ=255)
                                           aaCAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTg                           >  1:470834/1‑71 (MQ=255)
                                           aaCAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttcttc                             <  1:3412815/69‑1 (MQ=255)
                                           aaCAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttcttc                             <  1:2816182/69‑1 (MQ=255)
                                              aGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTggg                         >  1:3946538/1‑68 (MQ=255)
                                              aGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTggg                         >  1:244248/1‑68 (MQ=255)
                                              aGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGt                                                          <  1:2123610/37‑1 (MQ=255)
                                              aGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCg                         >  1:900169/1‑70 (MQ=255)
                                                 acaGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                     <  1:551815/71‑1 (MQ=255)
                                                 acaGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                     <  1:1270859/71‑1 (MQ=255)
                                                  caggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                     >  1:1122091/1‑70 (MQ=255)
                                                  caggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAg                     >  1:2450722/1‑70 (MQ=255)
                                                  caggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGt                    <  1:1360995/71‑1 (MQ=255)
                                                  caggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGt                    <  1:982072/71‑1 (MQ=255)
                                                    ggcaggGTCATGATAATCCCTGTACGGAAGTAATATc                                                    >  1:3410296/1‑37 (MQ=255)
                                                    ggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTAc                  >  1:3790670/1‑71 (MQ=255)
                                                    ggcaggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTAc                  >  1:505196/1‑71 (MQ=255)
                                                      caggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGt                >  1:2703927/1‑71 (MQ=255)
                                                       aggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAg                                        <  1:3383163/46‑1 (MQ=255)
                                                       aggGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTg               >  1:1778612/1‑71 (MQ=255)
                                                        cagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGc              <  1:1469196/69‑1 (MQ=255)
                                                        cagTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATGc              <  1:2889520/69‑1 (MQ=255)
                                                         agTCATGACAATGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATATTTTTCTGGGCAAGCACATg               >  1:263311/2‑69 (MQ=255)
                                                           tCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGAt                                          <  1:2653800/40‑1 (MQ=255)
                                                            cATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATAttc                                >  1:434815/1‑49 (MQ=255)
                                                             aTGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGc           >  1:3671796/1‑69 (MQ=255)
                                                             aTGACAATGCCGGTACGGAAGTAATATCCACAAGTGATTGTCATATTTTTCTGGGCAAGCACATGCAGCCa         >  1:2030701/1‑71 (MQ=255)
                                                               gATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCa                                     >  1:3665270/1‑41 (MQ=255)
                                                                aTAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGt                >  1:3574714/1‑61 (MQ=255)
                                                                 tAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCagag      >  1:2790014/1‑70 (MQ=255)
                                                                 caaTGCCGGTACGGAAGTAATATCCCCAAGTGATTGTCATAttt                                >  1:1889788/2‑43 (MQ=16)
                                                                   aTCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCAGAgta    <  1:3827742/70‑1 (MQ=255)
                                                                    tCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCAGAgtagc  >  1:1824913/1‑71 (MQ=255)
                                                                    tCCCTCTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGaa                       <  1:3702156/50‑1 (MQ=255)
                                                                     |                                                                     
CAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAGTCATATTCTTCTGCGAAAGTACGTGCAGCCAGAGTAGC  >  minE/2595311‑2595449

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