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 2,595,319 A→C 34.1% F427V (TTC→GTC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,3190AC34.1% 96.5 / 137.2 135F427V (TTC→GTC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base A (37/52);  new base C (26/20);  total (63/72)
Fisher's exact test for biased strand distribution p-value = 1.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

Only 100 of 142 total aligned reads displayed.

CGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGT  >  minE/2595249‑2595385
                                                                      |                                                                  
cgcgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaa                                                                    <  1:2640712/71‑1 (MQ=255)
cgcgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaa                                                                    <  1:4988950/71‑1 (MQ=255)
 gcgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaaa                                                                   <  1:976199/71‑1 (MQ=255)
   gACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:1384827/71‑1 (MQ=255)
    aCGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaaa                                                                   >  1:3725178/1‑68 (MQ=255)
    aCGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaaa                                                                   >  1:1645505/1‑68 (MQ=255)
       tGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAgagaga                                                             <  1:3901486/71‑1 (MQ=255)
         ccGCAGGCGGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACg                                                           <  1:4105189/71‑1 (MQ=255)
          cacAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgc                                                          >  1:3576424/3‑70 (MQ=255)
            cAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAg                                                        <  1:2406121/71‑1 (MQ=255)
             aGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAgc                                                       >  1:61564/1‑71 (MQ=255)
               gCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAgcgc                                                     <  1:455331/71‑1 (MQ=255)
                   ggTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                               >  1:1329552/1‑57 (MQ=255)
                   ggTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                               >  1:2444134/1‑57 (MQ=255)
                    gTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAgc                                                 <  1:3826773/70‑1 (MQ=255)
                     ttGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgcc                                                         <  1:1653857/61‑3 (MQ=255)
                     ttGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgcgc                                               <  1:340183/71‑1 (MQ=255)
                      tgtgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgcgc                                               <  1:4702643/70‑1 (MQ=255)
                       gtgATAAATGCTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGca                                              <  1:4087390/70‑1 (MQ=255)
                        tgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:954753/50‑1 (MQ=255)
                        tgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:2989208/50‑1 (MQ=255)
                         gATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggc                                            >  1:4396535/1‑70 (MQ=255)
                         gATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:37804/49‑1 (MQ=255)
                         gATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:44393/49‑1 (MQ=255)
                         gATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:1982257/49‑1 (MQ=255)
                         gATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:3650500/49‑1 (MQ=255)
                          aTAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACag                                                                  >  1:3007442/1‑47 (MQ=255)
                          aTAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACag                                                                  >  1:3614619/1‑47 (MQ=255)
                          aTAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAg                                                  >  1:3306303/1‑63 (MQ=255)
                           tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:3409390/47‑1 (MQ=255)
                           tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                                 <  1:4723629/47‑1 (MQ=255)
                           tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccag                                         <  1:2410854/71‑1 (MQ=255)
                           tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagcca                                          <  1:574231/70‑1 (MQ=255)
                            agaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAg                                                  <  1:5335149/59‑1 (MQ=255)
                            aaaTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGaa                                                                    >  1:4359505/1‑43 (MQ=255)
                            aaaTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                                        >  1:3462899/1‑71 (MQ=255)
                            aaaTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                                        >  1:3958727/1‑71 (MQ=255)
                            aaaTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                                        >  1:3469632/1‑71 (MQ=255)
                              aTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGTGCCAGCGCAGCCAGCGt                                      >  1:4839064/1‑71 (MQ=255)
                              aTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGt                                      >  1:3468783/1‑71 (MQ=255)
                              aTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAgcg                                                >  1:939264/1‑61 (MQ=255)
                              aTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAgcg                                                >  1:544843/1‑61 (MQ=255)
                               tGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTc                                     <  1:5228961/71‑1 (MQ=255)
                                ggTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGtga                                    >  1:2836887/1‑69 (MQ=255)
                                   aaTGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTcaca                                  >  1:1251148/1‑70 (MQ=255)
                                     tGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                            <  1:155170/58‑1 (MQ=255)
                                      gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTa                                                         >  1:2370715/1‑44 (MQ=255)
                                      gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                            >  1:2083160/1‑57 (MQ=255)
                                      gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                            >  1:2162843/1‑57 (MQ=255)
                                       ttGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGGGCAGCCAGCGTCACAAACAg                             >  1:5265201/1‑71 (MQ=255)
                                       ttGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAg                             >  1:287879/1‑71 (MQ=255)
                                       ttGCTCATATCAGTATCTAATTACAAAGTGACagag                                                                >  1:5415446/1‑36 (MQ=37)
                                       ttGCTCATATCAGTATCTAATTACAAAGTGACaga                                                                 >  1:837759/1‑35 (MQ=37)
                                       ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                              <  1:1086304/70‑1 (MQ=255)
                                       ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                              <  1:4281743/70‑1 (MQ=255)
                                       ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                              <  1:5067645/70‑1 (MQ=255)
                                       ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                              <  1:3899196/70‑1 (MQ=255)
                                       ttGCTCAAATCAGTATCTAATTACAAAGTGACagag                                                                >  1:5500292/1‑36 (MQ=255)
                                          cTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGcac                          <  1:2572734/71‑1 (MQ=255)
                                          cTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGcac                          <  1:844464/71‑1 (MQ=255)
                                          cTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGca                           <  1:1061871/70‑1 (MQ=255)
                                            cATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGcaccg                        >  1:4169565/1‑69 (MQ=255)
                                             atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                              <  1:541780/64‑1 (MQ=255)
                                             atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                              <  1:2459377/64‑1 (MQ=255)
                                             atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                              <  1:2809995/64‑1 (MQ=255)
                                             atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcagg                       >  1:4622462/1‑71 (MQ=255)
                                              tatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgc                                                 <  1:5650733/44‑1 (MQ=255)
                                              tatCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggcca                                          <  1:4603532/51‑1 (MQ=255)
                                              tatCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggcca                                          <  1:5087646/51‑1 (MQ=255)
                                              tatCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggcca                                          <  1:4323806/51‑1 (MQ=255)
                                               atCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                              >  1:2065172/1‑62 (MQ=255)
                                                tCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggca                     <  1:1859326/70‑1 (MQ=255)
                                                tCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                                        >  1:124132/1‑50 (MQ=255)
                                                  aGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAggg                  <  1:977500/71‑1 (MQ=255)
                                                    tATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGca                           <  1:3053832/60‑1 (MQ=255)
                                                      tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAg                             >  1:705235/1‑56 (MQ=255)
                                                      tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAg                             >  1:3134278/1‑56 (MQ=255)
                                                      tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcag                    <  1:4290259/65‑1 (MQ=255)
                                                      tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcag                    <  1:3355540/65‑1 (MQ=255)
                                                      tctaATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccag                                         <  1:2731350/44‑1 (MQ=12)
                                                      tctaATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCAt              >  1:1518678/1‑71 (MQ=255)
                                                          aTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGac           >  1:1737157/1‑69 (MQ=255)
                                                          aTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGac           <  1:3521973/70‑2 (MQ=255)
                                                          aTTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCATGac           >  1:4377325/1‑69 (MQ=255)
                                                          aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATg             <  1:2284194/68‑1 (MQ=255)
                                                          aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGAt           <  1:4851837/70‑1 (MQ=255)
                                                          aTTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATa          <  1:5540100/71‑1 (MQ=255)
                                                           ttACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                              <  1:4860878/50‑1 (MQ=255)
                                                           ttACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATaa         <  1:308626/71‑1 (MQ=255)
                                                            tACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcag                    <  1:5680226/59‑1 (MQ=255)
                                                             aCAAAGTGAAAGAGAGACGTAGCGCCAGCTCAGCCAGCGTCACAAAc                               >  1:1909327/1‑47 (MQ=255)
                                                             aCAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGa            >  1:4675637/1‑66 (MQ=255)
                                                              cAAAGTGAAAGAGAGACGTAGCGCCAGCTcagcca                                          >  1:1783513/1‑35 (MQ=255)
                                                              cAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATcc      >  1:1603561/1‑71 (MQ=255)
                                                               aaaGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGcac                          <  1:4110322/50‑1 (MQ=255)
                                                                aaGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcagg                   >  1:2154353/1‑56 (MQ=255)
                                                                 aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg   <  1:4786190/71‑1 (MQ=255)
                                                                 aGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg   <  1:1826622/71‑1 (MQ=255)
                                                                  gTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg   >  1:1153276/1‑70 (MQ=255)
                                                                  gTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTg   >  1:5256164/1‑70 (MQ=255)
                                                                      |                                                                  
CGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCATGATAATCCCTGT  >  minE/2595249‑2595385

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