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 2,595,306 C→A 33.3% intergenic (‑11/+2) arsC ← / ← arsB arsenate reductase/arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,3060CA33.3% 133.1 / 62.4 84intergenic (‑11/+2)arsC/arsBarsenate reductase/arsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base C (29/27);  new base A (9/19);  total (38/46)
Fisher's exact test for biased strand distribution p-value = 1.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

TCCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGA  >  minE/2595237‑2595375
                                                                     |                                                                     
tcCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                      >  1:1889602/1‑71 (MQ=255)
tcCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                      >  1:756080/1‑71 (MQ=255)
 ccAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCAt                                                                     >  1:740956/1‑71 (MQ=255)
  cAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTAtctc                                                                       <  1:2656478/68‑1 (MQ=255)
  cAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTAtctc                                                                       <  1:1560621/68‑1 (MQ=255)
  cAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                      <  1:3209063/69‑1 (MQ=255)
   aGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTa                                                                   <  1:99255/71‑1 (MQ=255)
    gCGTGTTGCGTGAGGTGCTACAGGCCGGGTTGTGATAGATGGTAATGTTGATCATATCAGTATCTAATTa                                                                   >  1:3424739/1‑70 (MQ=255)
    gCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTa                                                                   >  1:2326959/1‑70 (MQ=255)
    gCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTAc                                                                  <  1:2753213/71‑1 (MQ=255)
    gCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTa                                                                   >  1:1590420/1‑70 (MQ=255)
     cGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACa                                                                 <  1:3436311/71‑1 (MQ=255)
           aCGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTg                                                            >  1:3637173/1‑70 (MQ=255)
           aCGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTg                                                            <  1:754711/70‑1 (MQ=255)
            cgcgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTg                                                            <  1:1221495/69‑1 (MQ=255)
            cgcgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGa                                                           >  1:168189/1‑70 (MQ=255)
             gcgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaaa                                                         <  1:2410225/71‑1 (MQ=255)
              cgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAag                                                        <  1:1810013/71‑1 (MQ=255)
               gACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                       <  1:2542776/71‑1 (MQ=255)
                aggTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACaga                                                       <  1:2437832/68‑1 (MQ=255)
                 ggTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTg                                                            <  1:529118/63‑1 (MQ=255)
                 ggTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATAAGTATCTAATTACAAAGTg                                                            <  1:813768/63‑1 (MQ=255)
                 cGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                     <  1:2427159/71‑1 (MQ=255)
                 cGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                       >  1:697413/1‑69 (MQ=255)
                 cGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                       >  1:1999142/1‑69 (MQ=255)
                   tGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                       <  1:716150/67‑1 (MQ=255)
                   tGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACa                                                                 <  1:3883971/57‑1 (MQ=255)
                    gCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGAc                                                  >  1:2170751/1‑71 (MQ=255)
                    gCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGAc                                                  >  1:655747/1‑71 (MQ=255)
                     ccGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACg                                                 >  1:1950270/1‑71 (MQ=255)
                     ccGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACg                                                 >  1:2712208/1‑71 (MQ=255)
                     ccGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACg                                                 >  1:2716847/1‑71 (MQ=255)
                      cGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                      <  1:949235/49‑1 (MQ=255)
                       acAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgcc                                               <  1:1770789/70‑3 (MQ=255)
                        cAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACaga                                                       >  1:3912182/1‑62 (MQ=255)
                         aGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAgc                                             <  1:3577484/71‑1 (MQ=255)
                           gCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAgcgc                                           <  1:828145/71‑1 (MQ=255)
                            ccGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                     >  1:1028909/1‑60 (MQ=255)
                               ggTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAgc                                       >  1:3680107/1‑71 (MQ=255)
                               ggTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAg                                        >  1:2377166/1‑70 (MQ=255)
                                gTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaaa                                                         <  1:1481245/52‑1 (MQ=255)
                                gTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaaa                                                         <  1:1473824/52‑1 (MQ=255)
                                gTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgcg                                      <  1:523028/71‑1 (MQ=255)
                                gTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgcg                                      <  1:3544600/71‑1 (MQ=255)
                                  tgtgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgcg                                      >  1:1493478/1‑69 (MQ=255)
                                   gtgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcag                                   >  1:2170121/1‑71 (MQ=255)
                                   gtgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcag                                   >  1:2165543/1‑71 (MQ=255)
                                    tgATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggc                                  <  1:3812469/71‑1 (MQ=255)
                                    tgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAg                                        >  1:88660/1‑65 (MQ=255)
                                     gATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTg                                                            <  1:297475/44‑1 (MQ=38)
                                      aTAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagcc                                 <  1:2661785/70‑1 (MQ=255)
                                        agaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACagaga                                                     >  1:1274129/3‑48 (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)
                                           tGGTAATGTTGCTCATATCAGTATCTCATTACAAAg                                                              >  1:3343263/1‑36 (MQ=255)
                                              tAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTgaca                        <  1:820837/71‑1 (MQ=255)
                                                aTGTTGCTCATATCAGTATCTCATTACAAAGTGAAagagag                                                    >  1:3250760/1‑41 (MQ=255)
                                                aTGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACaa                       <  1:3403041/70‑1 (MQ=255)
                                                 tGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                     <  1:735226/39‑1 (MQ=255)
                                                 tGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACaaa                      >  1:3213169/1‑70 (MQ=255)
                                                 tGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGt                            <  1:3184317/64‑1 (MQ=255)
                                                 tGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAAc                     <  1:3837190/71‑1 (MQ=255)
                                                  gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACg                                                 <  1:750201/42‑1 (MQ=255)
                                                  gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTcaca                        <  1:88415/67‑1 (MQ=255)
                                                  gTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                              <  1:3459494/61‑2 (MQ=255)
                                                  gTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                              <  1:3763272/61‑2 (MQ=255)
                                                  gTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACaa                       >  1:1310177/1‑68 (MQ=255)
                                                    tGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAg                   >  1:2276807/1‑70 (MQ=255)
                                                     gCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGt                                                >  1:3826960/1‑40 (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)
                                                                     |                                                                     
TCCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGA  >  minE/2595237‑2595375

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