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 2,596,130 G→A 26.5% V156V (GTC→GTT)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,596,1300GA26.5% 108.9 / 39.4 64V156V (GTC→GTT) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (21/26);  new base A (7/10);  total (28/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCACCGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCT  >  minE/2596062‑2596199
                                                                    |                                                                     
aTCACCGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGAc                                                                     <  1:855573/71‑1 (MQ=255)
 tCACCGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGAc                                                                     >  1:228468/1‑70 (MQ=255)
    ccGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATa                                                                 <  1:1929019/71‑1 (MQ=255)
     cGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATaa                                                                <  1:453881/71‑1 (MQ=255)
      gAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAg                                                               >  1:1513322/1‑71 (MQ=255)
             aTTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAgg                                                        >  1:1371377/1‑71 (MQ=255)
                cgcgAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTg                                                     >  1:274491/1‑71 (MQ=255)
                 gcgAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTgg                                                    >  1:1117304/1‑71 (MQ=255)
                 gcgAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTgg                                                    <  1:1896383/71‑1 (MQ=255)
                  cgAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGAc                                                                     <  1:2733741/53‑1 (MQ=255)
                  cgAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGAc                                                                     <  1:2492156/53‑1 (MQ=255)
                  cgAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGAc                                                                     <  1:2396547/53‑1 (MQ=255)
                   gAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCg                                                  <  1:2789780/71‑1 (MQ=255)
                    aaaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGc                                                              >  1:744467/1‑58 (MQ=255)
                     aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                                 >  1:2877939/1‑70 (MQ=255)
                     aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                                 >  1:635676/1‑70 (MQ=255)
                     aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                                 >  1:2715622/1‑70 (MQ=255)
                     aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGt                                                <  1:203151/71‑1 (MQ=255)
                       gCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTAt                                              <  1:2529413/71‑1 (MQ=255)
                        ccGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATc                                             >  1:3677093/1‑71 (MQ=255)
                         cGAGGCCAAAGAAATCAGCGTAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCg                                            <  1:3030136/71‑1 (MQ=255)
                           aGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGc                                          <  1:1731717/71‑1 (MQ=255)
                             gCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCaa                                        >  1:2084086/1‑71 (MQ=255)
                              ccAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                       <  1:2061612/71‑1 (MQ=255)
                              ccAAAGAAATAAGCGGAAACGATATTCACCAGGTTGGAGAc                                                                     <  1:1967548/41‑1 (MQ=255)
                               cgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTa                                               <  1:2746529/60‑1 (MQ=255)
                                gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACaa                                                                   >  1:239345/2‑41 (MQ=12)
                                gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAAtg                                                                 <  1:881907/42‑2 (MQ=16)
                                gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAtaa                                     <  1:1599426/70‑3 (MQ=255)
                                aaaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATaa                                                                <  1:2609176/44‑1 (MQ=255)
                                aaaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATaa                                                                <  1:2669200/44‑1 (MQ=255)
                                 aagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATaaa                                    <  1:2122001/71‑1 (MQ=255)
                                 aaGAAATCAGCGGAAACGATATTCACCAGGTTGgaga                                                                      >  1:1524877/1‑37 (MQ=255)
                                 aaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGaa                                    >  1:333578/1‑71 (MQ=255)
                                 aaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGaa                                    >  1:3449102/1‑71 (MQ=255)
                                  aGAAGTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATct                                            >  1:675806/1‑61 (MQ=255)
                                  aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCg                                                  >  1:3522283/1‑56 (MQ=255)
                                  aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAAt                                   >  1:3510425/1‑71 (MQ=255)
                                           cGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGgccgc                           >  1:70191/1‑70 (MQ=255)
                                            ggAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGTTATCGGCAATGAATCCGGCCGCCa                         >  1:3568100/1‑71 (MQ=255)
                                               gaCGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAtga                      <  1:2985791/70‑3 (MQ=255)
                                                aCGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGgcc                             >  1:56520/1‑63 (MQ=255)
                                                aCGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCAc                     <  1:1297938/71‑1 (MQ=255)
                                                aCGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAtaa                                     >  1:2573727/1‑53 (MQ=255)
                                                  gATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAt                                       <  1:2702354/51‑1 (MQ=255)
                                                  gATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGAcaa                   <  1:2419478/71‑3 (MQ=255)
                                                  gATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGAca                    <  1:1542783/70‑2 (MQ=255)
                                                    tatTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAAc                 >  1:2097649/1‑71 (MQ=255)
                                                      ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGt                                                <  1:3217631/38‑1 (MQ=255)
                                                      ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCAc                     <  1:487693/65‑1 (MQ=255)
                                                       tCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGaa                  <  1:3465117/67‑1 (MQ=255)
                                                       tCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGc               >  1:3485191/1‑70 (MQ=255)
                                                         aCCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCg                                <  1:3889235/51‑1 (MQ=255)
                                                         aCCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCa             <  1:819963/70‑1 (MQ=255)
                                                          ccAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATcc                                 >  1:991115/1‑49 (MQ=255)
                                                          ccAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgt           <  1:307056/71‑2 (MQ=255)
                                                           cAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGgccgcc                          <  1:416266/55‑1 (MQ=255)
                                                           cAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCg          <  1:3783559/71‑1 (MQ=255)
                                                            aGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTgca                             >  1:3436126/1‑50 (MQ=255)
                                                            aGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtgt         >  1:2497266/1‑71 (MQ=255)
                                                             ggTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtgtc        >  1:3315800/1‑70 (MQ=255)
                                                              gTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                       <  1:1555969/39‑1 (MQ=255)
                                                              gTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGc                                          <  1:955960/36‑1 (MQ=12)
                                                                 ggAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAg       >  1:1119177/1‑68 (MQ=255)
                                                                 ggAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTg     <  1:2402450/70‑1 (MQ=255)
                                                                  gagaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGc    <  1:2267886/70‑1 (MQ=255)
                                                                   agaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCgg                               <  1:58925/42‑1 (MQ=255)
                                                                   agaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCt  <  1:1856390/71‑1 (MQ=255)
                                                                    gaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGt         <  1:3057455/63‑1 (MQ=255)
                                                                    |                                                                     
ATCACCGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCT  >  minE/2596062‑2596199

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