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 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,823,628 G→A 6.6% intergenic (+373/+585) nrfG → / ← pheU heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,823,6280GA 6.6% 243.9 / 5.6 76intergenic (+373/+585)nrfG/pheUheme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe
Reads supporting (aligned to +/- strand):  ref base G (29/42);  new base A (3/2);  total (32/44)
Fisher's exact test for biased strand distribution p-value = 6.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.61e-01

CGGGGAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGC  >  minE/2823563‑2823695
                                                                 |                                                                   
cGGGGAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCgatgat                                                                <  1:1947899/71‑1 (MQ=255)
 ggggAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATa                                                               <  1:290874/71‑1 (MQ=255)
    gAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAAtt                                                            <  1:1493537/71‑1 (MQ=255)
     aaCGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTg                                                           >  1:2060586/1‑71 (MQ=255)
       cGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGc                                                          >  1:2727151/1‑70 (MQ=255)
       cGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGAAGATAAtt                                                            >  1:2665162/1‑68 (MQ=255)
        ggCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGcc                                                         <  1:2886774/70‑1 (MQ=255)
         gcgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCca                                                        >  1:1244555/1‑70 (MQ=255)
         gcgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCca                                                        >  1:630508/1‑70 (MQ=255)
         gcgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGAGATGATAATTGCcac                                                       <  1:2787839/71‑1 (MQ=255)
         gcgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGAGATGATAATTGCcac                                                       <  1:775409/71‑1 (MQ=255)
          cgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCcaca                                                      <  1:1960893/71‑1 (MQ=255)
          cgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCcaca                                                      <  1:1956652/71‑1 (MQ=255)
          cgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCcaca                                                      <  1:3018961/71‑1 (MQ=255)
          cgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCcac                                                       <  1:2916560/70‑1 (MQ=255)
                aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt                                                <  1:3577494/71‑1 (MQ=255)
                aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt                                                <  1:2788792/71‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCg                                                                     <  1:3486026/49‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCg                                                                     <  1:2877622/49‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCg                                                                     <  1:619154/49‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGc                                                          <  1:1867179/60‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGc                                                          <  1:3086150/60‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGc                                                          <  1:218860/60‑1 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtt                                               >  1:3201881/1‑71 (MQ=255)
                 ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt                                                <  1:2704701/70‑1 (MQ=255)
                  tGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtt                                               >  1:1010298/1‑70 (MQ=255)
                    aGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAttttt                                            <  1:2071530/71‑1 (MQ=255)
                      gAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTg                                                           >  1:1688219/1‑54 (MQ=255)
                      gAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTAc                                          >  1:2875047/1‑71 (MQ=255)
                       aaGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTAcc                                         <  1:2776127/71‑1 (MQ=255)
                         gTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCAt                                       >  1:1481003/1‑71 (MQ=255)
                           cattcatAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt                                                <  1:101338/60‑1 (MQ=255)
                            ttgcatAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCGCAACCTATTTTTACCATCta                                    <  1:85759/68‑1 (MQ=255)
                            ttgcatAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCta                                    <  1:308462/68‑1 (MQ=255)
                            attcatAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTa                                                 <  1:23571/58‑1 (MQ=255)
                            attcatAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTa                                                 <  1:2866217/58‑1 (MQ=255)
                            attcatAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCta                                    >  1:715736/1‑71 (MQ=255)
                            attcatAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCta                                    <  1:3241456/71‑1 (MQ=255)
                             ttcatAATAGAAACTCATTCGAAAAGGGACTGATGCGATGATAATTGCCACAACCTAt                                                <  1:419251/58‑1 (MQ=255)
                             ttcatAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTa                                                 <  1:946693/57‑1 (MQ=255)
                               catAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAttttt                                            <  1:2410764/60‑1 (MQ=255)
                               catAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAttttt                                            <  1:1759691/60‑1 (MQ=255)
                                 taataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGAt                               <  1:18906/71‑1 (MQ=255)
                                 taataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGAt                               <  1:679244/71‑1 (MQ=255)
                                 taataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGAt                               <  1:1696265/71‑1 (MQ=255)
                                  aataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATg                              >  1:2372673/1‑71 (MQ=255)
                                   ataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATg                              <  1:186396/70‑1 (MQ=255)
                                   ataGAAACTCATTCGAAAAGGGAATGATGCAATGATa                                                               >  1:52036/1‑37 (MQ=255)
                                   ataGAAACTCATTCGAAAAGGGAATGATGCAATGATa                                                               >  1:525423/1‑37 (MQ=255)
                                   ataGAAACTCATTCGAAAAGGGAATGATGCAATGATa                                                               >  1:1661641/1‑37 (MQ=255)
                                     aGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGt                           >  1:862554/1‑71 (MQ=255)
                                      gAAACTCATTCGAAAAGGGAATGATGCGATGATAATTg                                                           >  1:2870427/1‑38 (MQ=255)
                                      gAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt                          >  1:759764/1‑71 (MQ=255)
                                       aaaCTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttt                         <  1:2102222/71‑1 (MQ=255)
                                        aaCTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttt                         <  1:2097781/70‑1 (MQ=255)
                                              ttCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACa                  >  1:704633/1‑71 (MQ=255)
                                               tCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTA‑TTTTACCATCTATAGATGGGTTTATTTACata                >  1:873270/1‑71 (MQ=255)
                                                cGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtt                                               <  1:1457082/40‑1 (MQ=255)
                                                cGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtt                                               <  1:1039232/40‑1 (MQ=255)
                                                cGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtt                                               <  1:1472918/40‑1 (MQ=255)
                                                 gAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACatat               <  1:521945/71‑1 (MQ=255)
                                                  aaaaGGGAATGATGCGATGATAATTGCCACAACCTAtttt                                             >  1:3304967/1‑40 (MQ=255)
                                                  aaaaGGGAATGATGCGATGATAATTGCCACAACCTAtttt                                             >  1:432463/1‑40 (MQ=255)
                                                  aaaaGGGAATGATGCGATGATAATTGCCACAACCTAtttt                                             >  1:3154876/1‑40 (MQ=255)
                                                  aaaaGGGAATGATGCGATGATAATTGCCACAACCTAtttt                                             >  1:1896266/1‑40 (MQ=255)
                                                  aaaaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACatat               <  1:3030842/70‑1 (MQ=255)
                                                    aaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtattat            >  1:1406792/1‑71 (MQ=255)
                                                    aaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtattat            >  1:2509866/1‑71 (MQ=255)
                                                    aaGGGAATGATGCGATGATAATTGCCAAAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtattat            >  1:3722255/1‑71 (MQ=255)
                                                       ggAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCtata                                  >  1:1468036/1‑46 (MQ=255)
                                                       ggAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCtata                                  >  1:610821/1‑46 (MQ=255)
                                                       ggAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGAt                               <  1:3292087/49‑1 (MQ=255)
                                                        gAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt        <  1:2860248/71‑1 (MQ=255)
                                                         aaTGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt        >  1:1877847/1‑70 (MQ=255)
                                                         aaTGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTg       <  1:3244487/71‑1 (MQ=255)
                                                           tgatgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta                    >  1:798613/1‑56 (MQ=255)
                                                             atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATg   >  1:501453/1‑71 (MQ=255)
                                                             atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATg   <  1:2927680/71‑1 (MQ=255)
                                                              tgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGc  <  1:3144767/71‑1 (MQ=255)
                                                              tgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGc  <  1:309654/71‑1 (MQ=255)
                                                                 |                                                                   
CGGGGAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGC  >  minE/2823563‑2823695

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