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 2,596,136 A→G 28.3% L154L (CTT→CTC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,596,1360AG28.3% 86.2 / 42.1 60L154L (CTT→CTC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base A (20/23);  new base G (7/10);  total (27/33)
Fisher's exact test for biased strand distribution p-value = 7.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

CCGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACT  >  minE/2596066‑2596204
                                                                      |                                                                    
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)
               gAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCg                                                       <  1:2789780/71‑1 (MQ=255)
                aaaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGc                                                                   >  1:744467/1‑58 (MQ=255)
                 aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                                      >  1:2877939/1‑70 (MQ=255)
                 aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                                      >  1:2715622/1‑70 (MQ=255)
                 aaGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCgg                                                      >  1:635676/1‑70 (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)
                           cgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTa                                                    <  1:2746529/60‑1 (MQ=255)
                            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)
                             aaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGaa                                         >  1:3449102/1‑71 (MQ=255)
                             aaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGaa                                         >  1:333578/1‑71 (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)
                                                               aaaCAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACATAGGCCAGCGTCGTGccc       >  1:548452/3‑70 (MQ=255)
                                                                gaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGt              <  1:3057455/63‑1 (MQ=255)
                                                                 aCAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAGTGTCGTGccctg     <  1:2091714/71‑4 (MQ=255)
                                                                   aaTAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGcc        <  1:2481318/66‑1 (MQ=255)
                                                                    aTAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACt  <  1:868664/71‑1 (MQ=255)
                                                                      |                                                                    
CCGAGGCGTATTCGCGAAAGCCGAGGCCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACT  >  minE/2596066‑2596204

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A