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
A2 F28 I3 R2 122 64.1 3058059 97.6% 2984665 63.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 2,681,918 A→G R598R (CGT→CGC)  yhgF ← predicted transcriptional accessory protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,681,9180AG96.7% 206.2 / ‑1.6 60R598R (CGT→CGC) yhgFpredicted transcriptional accessory protein
Reads supporting (aligned to +/- strand):  ref base A (0/2);  new base G (27/31);  total (27/33)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

TTGATGATGTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTACGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCGTTC  >  minE/2681853‑2681983
                                                                 |                                                                 
ttGATGATGTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAg                                                              >  1:1908149/1‑71 (MQ=255)
  gatgatGTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGtt                                                            >  1:599123/1‑71 (MQ=255)
   atgatgTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAg                                                              >  1:2097140/1‑68 (MQ=255)
      atgTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgc                                                         <  1:2883076/70‑1 (MQ=255)
      atgTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgc                                                         <  1:1617682/70‑1 (MQ=255)
       tgTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCg                                                          >  1:1165873/1‑68 (MQ=255)
        gTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgctgc                                                      >  1:2626190/1‑71 (MQ=255)
           ggTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTACGCAGTTCGCTGCTGt                                                   <  1:929418/71‑1 (MQ=255)
                   tCGGCACACCGAATTTCTCATCAGTAAAGTCAGCCGCTTTCAGGTTGAGCAg                                                              >  1:1001842/1‑52 (MQ=38)
                   tCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAg                                                              >  1:1442826/1‑52 (MQ=255)
                     ggCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATc                                           >  1:371449/1‑69 (MQ=255)
                          acCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCtt                                    <  1:83202/71‑1 (MQ=255)
                           ccGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   <  1:1308157/71‑1 (MQ=255)
                           ccGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   <  1:1386050/71‑1 (MQ=255)
                           ccGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   <  1:521834/71‑1 (MQ=255)
                            cGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGt                                                   >  1:747388/1‑54 (MQ=255)
                            cGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   >  1:2047090/1‑70 (MQ=255)
                            cGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   >  1:2209382/1‑70 (MQ=255)
                             gAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   >  1:216488/1‑69 (MQ=255)
                              aaTTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTc                                                           <  1:465499/44‑1 (MQ=255)
                                tttCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgctg                                                       <  1:619000/46‑1 (MQ=255)
                                 ttCTCATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgctg                                                       >  1:2356943/1‑45 (MQ=255)
                                  tctcATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgctgct                                                     >  1:970054/1‑46 (MQ=255)
                                  tctcATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGc                             <  1:1252460/70‑1 (MQ=255)
                                  tctcATCAGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGc                             <  1:806582/70‑1 (MQ=255)
                                     catcaGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCa                                 >  1:546346/1‑63 (MQ=255)
                                      atcaGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCgc                                                         >  1:579862/1‑38 (MQ=255)
                                      atcaGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCctgc                         <  1:2249546/70‑1 (MQ=255)
                                      atcaGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTCACCCATCAGATCTTTCAGTGCctgct                        >  1:496730/1‑71 (MQ=255)
                                       tcaGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCctgctg                       >  1:1906659/1‑71 (MQ=255)
                                       tcaGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCctgctg                       <  1:2681329/71‑1 (MQ=255)
                                        caGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCtgt                      >  1:2940550/1‑71 (MQ=255)
                                         aGTAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCtgt                      <  1:2581029/70‑1 (MQ=255)
                                           tAAAGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGtt                   <  1:1104745/71‑1 (MQ=255)
                                            aaaGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGt                                                   <  1:529921/38‑1 (MQ=255)
                                             aaGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtgc                 >  1:210742/1‑71 (MQ=255)
                                             aaGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtg                  >  1:2958919/1‑70 (MQ=255)
                                              aGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCa                                 >  1:2576798/1‑54 (MQ=255)
                                              aGTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtgct                <  1:2334720/71‑1 (MQ=255)
                                               gTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtgct                <  1:754572/70‑1 (MQ=255)
                                               gTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtgct                <  1:2543504/70‑1 (MQ=255)
                                               gTCAGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtgct                <  1:2464189/70‑1 (MQ=255)
                                                  aGACGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTtgctgc              >  1:2695942/1‑69 (MQ=255)
                                                    aCGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTc                                  <  1:1972467/47‑1 (MQ=255)
                                                    aCGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTc                                  <  1:1968845/47‑1 (MQ=255)
                                                    aCGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAg           <  1:2138753/70‑1 (MQ=255)
                                                    aCGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGa          <  1:2115663/71‑1 (MQ=255)
                                                     cGCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCatgctg                       >  1:2250766/1‑57 (MQ=255)
                                                     cGCTTTCAGGTTACGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGaa         <  1:90864/71‑1 (MQ=255)
                                                      gCTTTCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAAt        <  1:1710434/71‑1 (MQ=255)
                                                        tttCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCctgctg                       <  1:2327832/54‑1 (MQ=255)
                                                        tttCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGa          <  1:796556/67‑1 (MQ=255)
                                                         ttCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   <  1:735991/41‑1 (MQ=255)
                                                         ttCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCttt                                   <  1:1171702/41‑1 (MQ=255)
                                                         ttCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCg     >  1:2666966/1‑71 (MQ=255)
                                                         ttCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCg     >  1:107288/1‑71 (MQ=255)
                                                          tCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCg     <  1:2771338/70‑1 (MQ=255)
                                                          tCAGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCg     <  1:1847669/70‑1 (MQ=255)
                                                            aGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCa                                 >  1:297735/1‑40 (MQ=255)
                                                            aGGTTGCGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCGTTc  <  1:898017/71‑1 (MQ=255)
                                                                 |                                                                 
TTGATGATGTCGGTTACCGTCGGCACACCGAATTTCTCATCAGTAAAGTCAGACGCTTTCAGGTTACGCAGTTCGCTGCTGTTACCCATCAGATCTTTCAGTGCCTGCTGTGTTGCTGCCAGAATGCGTTC  >  minE/2681853‑2681983

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