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 2,595,341 A→G 21.7% A419A (GCT→GCC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,3410AG21.7% 127.9 / 34.8 69A419A (GCT→GCC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base A (22/32);  new base G (8/7);  total (30/39)
Fisher's exact test for biased strand distribution p-value = 3.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.48e-01

GTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAG  >  minE/2595272‑2595411
                                                                     |                                                                      
gtgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcag                                                                       >  1:2170121/1‑71 (MQ=255)
gtgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcag                                                                       >  1:2165543/1‑71 (MQ=255)
 tgATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggc                                                                      <  1:3812469/71‑1 (MQ=255)
   aTAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagcc                                                                     <  1:2661785/70‑1 (MQ=255)
      gaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccagag                                                                 <  1:3069942/70‑3 (MQ=255)
      gaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccagag                                                                 <  1:3065263/70‑3 (MQ=255)
      gaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                                                                  <  1:570129/69‑2 (MQ=255)
      aaTGGTAATGTTGCTCATAACAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCg                                                                 <  1:2762614/71‑1 (MQ=255)
       aTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                                                      >  1:3927779/1‑65 (MQ=255)
       aTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGt                                                                >  1:1962623/1‑71 (MQ=255)
       aTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGt                                                                <  1:570583/71‑1 (MQ=255)
           tAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTgaca                                                            <  1:820837/71‑1 (MQ=255)
             aTGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACaa                                                           <  1:3403041/70‑1 (MQ=255)
              tGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACaaa                                                          >  1:3213169/1‑70 (MQ=255)
              tGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGt                                                                <  1:3184317/64‑1 (MQ=255)
              tGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAAc                                                         <  1:3837190/71‑1 (MQ=255)
               gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTcaca                                                            <  1:88415/67‑1 (MQ=255)
               gTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                                                                  <  1:3763272/61‑2 (MQ=255)
               gTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                                                                  <  1:3459494/61‑2 (MQ=255)
               gTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACaa                                                           >  1:1310177/1‑68 (MQ=255)
                 tGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAg                                                       >  1:2276807/1‑70 (MQ=255)
                  gCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGc                                                      <  1:3681216/70‑1 (MQ=255)
                   cTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGca                                                     >  1:3836341/1‑70 (MQ=255)
                    tCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGc                                                      <  1:3183512/68‑1 (MQ=255)
                    tCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGcacc                                                   >  1:81486/1‑70 (MQ=255)
                     cATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACaaa                                                          >  1:559926/1‑63 (MQ=255)
                      atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcagg                                                 >  1:429480/1‑71 (MQ=255)
                      atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcag                                                  <  1:3586054/70‑1 (MQ=255)
                      atatCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACaaa                                                          <  1:3632121/62‑1 (MQ=255)
                         tCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggca                                               <  1:383569/70‑1 (MQ=255)
                         tCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggca                                               <  1:2755530/70‑1 (MQ=255)
                           aGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAggg                                            >  1:10222/1‑71 (MQ=255)
                             tATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGt                                           >  1:1847403/1‑70 (MQ=255)
                               tctcTTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCa                                         <  1:2217803/70‑1 (MQ=255)
                                  cATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGa                                      >  1:2259166/1‑70 (MQ=255)
                                   aatACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATa                                    <  1:3616152/69‑1 (MQ=255)
                                   aTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGac                                     <  1:2522409/70‑2 (MQ=255)
                                   aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCAt                                        <  1:737032/67‑1 (MQ=255)
                                   aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCAt                                        <  1:3633394/67‑1 (MQ=255)
                                    ttACAAAGTGAAAGAGAGACGTAGCGCCAGCTCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATaa                                   <  1:3458706/71‑1 (MQ=255)
                                    ttACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                                                                  <  1:2848514/40‑1 (MQ=255)
                                    ttACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                                                                  <  1:955717/40‑1 (MQ=255)
                                    ttACAAACTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATaa                                   <  1:3817304/71‑1 (MQ=255)
                                     tACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAAt                                  >  1:2860903/1‑71 (MQ=255)
                                       cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                >  1:3770257/1‑71 (MQ=255)
                                       cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc                                <  1:2732030/71‑1 (MQ=255)
                                       cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATc                                 <  1:2117169/70‑1 (MQ=255)
                                       cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATc                                 <  1:1120769/70‑1 (MQ=255)
                                        aaaGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTc                                                               <  1:2263014/39‑1 (MQ=255)
                                          aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                             >  1:3918337/1‑71 (MQ=255)
                                          aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                             <  1:743724/71‑1 (MQ=255)
                                          aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg                             <  1:3201099/71‑1 (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       >  1:2844051/1‑67 (MQ=255)
                                                                 gcgcGGCCAGAGTGACAAACAGCACCGGCACAGTCATGACAATGCCGGTACGGAAGTAATATCCCCaagt       >  1:3247024/1‑67 (MQ=255)
                                                                  cgcAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGa     >  1:681841/1‑71 (MQ=255)
                                                                    cagccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATa   <  1:1171195/71‑1 (MQ=255)
                                                                     agccagcGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAg  >  1:1978763/1‑71 (MQ=255)
                                                                     |                                                                      
GTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGTACGGAAGTAATATCCCCAGCTGATAG  >  minE/2595272‑2595411

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