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 1,826,285 A→G 32.2% I13I (ATT→ATC)  hydN ← formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,826,2850AG32.2% 171.4 / 117.7 143I13I (ATT→ATC) hydNformate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
Reads supporting (aligned to +/- strand):  ref base A (60/37);  new base G (25/21);  total (85/58)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 146 total aligned reads displayed.

GGTCAGCGATGCACAGTCCTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCC  >  minE/1826216‑1826354
                                                                     |                                                                     
ggTCAGCGATGCACAGTCCTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCaa                                                                      <  1:2852499/71‑1 (MQ=255)
    aGCGATGCACAGTCCTGATTTTCCTGATGAGAAACCACTCACGCTACTACACAGGTACGGCAACCAATACa                                                                  >  1:508002/1‑71 (MQ=255)
    aGCGATGCACAGTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATAc                                                                   <  1:3326430/70‑1 (MQ=255)
    aGCGATGCACAGTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACa                                                                  >  1:1007127/1‑71 (MQ=255)
      cGATGCACAGTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACAtt                                                                <  1:1007139/71‑1 (MQ=255)
      cGATGCACAGTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACAtt                                                                <  1:4151053/71‑1 (MQ=255)
        aTGCACAGTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTa                                                              <  1:1973093/71‑1 (MQ=255)
             caatCCTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgc                                                         <  1:4541114/68‑1 (MQ=255)
             caatCCTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgc                                                         <  1:3192130/68‑1 (MQ=255)
             caatCCTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgc                                                         <  1:1102946/68‑1 (MQ=255)
              aatCCTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgca                                                        >  1:649410/3‑70 (MQ=255)
               gTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACt                                                            >  1:133643/1‑66 (MQ=255)
               gTCCTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACt                                                            >  1:4059290/1‑66 (MQ=255)
               atCCTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgcat                                                       >  1:4393609/2‑69 (MQ=255)
               atCCTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgcat                                                       >  1:1623890/2‑69 (MQ=255)
               atCCTGAATCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTcgcat                                                       <  1:1165970/70‑3 (MQ=255)
                  cTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                    >  1:4335482/1‑71 (MQ=255)
                  cTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                    >  1:880577/1‑71 (MQ=255)
                  cTGATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACAt                                                                 >  1:1394768/1‑58 (MQ=255)
                  cTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACAt                                                                 >  1:1124460/1‑58 (MQ=255)
                  cTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACAt                                                                 >  1:4947987/1‑58 (MQ=255)
                  cTGATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATccg                                                    >  1:1523518/1‑69 (MQ=255)
                    gATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACt                                                            >  1:3799546/1‑61 (MQ=255)
                    gATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACt                                                            >  1:3681554/1‑61 (MQ=255)
                    gATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGc                                                   >  1:4850430/1‑70 (MQ=255)
                     aTTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCaa                                                 >  1:5036326/1‑71 (MQ=255)
                     aTTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCa                                                  <  1:2285167/70‑1 (MQ=255)
                     aTTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACAt                                                                 >  1:2524375/1‑55 (MQ=255)
                     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGc                                                   <  1:3267245/69‑1 (MQ=255)
                     aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCa                                                  <  1:3064599/70‑1 (MQ=255)
                         tCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                             >  1:4631497/1‑71 (MQ=255)
                           atgatgcGACACTGCGCAAGCCACTTCACAGGTACGGCACCCGATACATTTCGTCGCATCCGCaataata                                            >  1:4067795/2‑69 (MQ=255)
                           atgatgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                            <  1:5204141/69‑2 (MQ=255)
                           atgatgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAataa                                              <  1:2683741/67‑3 (MQ=255)
                             gatgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaac                                         >  1:3092677/1‑70 (MQ=255)
                              atgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACAttt                                                               >  1:1321704/1‑48 (MQ=19)
                              atgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                        >  1:860411/1‑71 (MQ=255)
                              atgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                        >  1:5350741/1‑71 (MQ=255)
                              atgaGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaaa                                         <  1:2500988/70‑1 (MQ=255)
                              atgaGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                        >  1:4810690/1‑71 (MQ=255)
                              atgaGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                        >  1:2564220/1‑71 (MQ=255)
                               tgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACg                                       >  1:1061345/1‑71 (MQ=255)
                                gagaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACgg                                      >  1:4285982/1‑71 (MQ=255)
                                 agaAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                     >  1:4197328/1‑71 (MQ=255)
                                  gaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                     >  1:3715697/1‑70 (MQ=255)
                                   aaaCCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtc                                   <  1:1646897/71‑1 (MQ=255)
                                   aaaCCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                    <  1:5528802/54‑1 (MQ=255)
                                     actgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcat                                 >  1:1878049/4‑71 (MQ=255)
                                     aCCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCa                                                  >  1:1485272/1‑54 (MQ=255)
                                     aCCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCa                                                  >  1:3727298/1‑54 (MQ=255)
                                      ctgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatg                                <  1:437939/69‑2 (MQ=255)
                                       tgcgcAAGCCACTTCACAGGTACGGCAACCGATACAtt                                                                <  1:3410947/37‑1 (MQ=25)
                                       tgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAat                                                <  1:863635/53‑1 (MQ=255)
                                        gcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                            >  1:685906/1‑56 (MQ=255)
                                        gcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataat                                             >  1:4456837/1‑56 (MQ=255)
                                        gcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatgat                              >  1:3055161/1‑68 (MQ=255)
                                        gcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatgat                              >  1:3596661/1‑68 (MQ=255)
                                        acgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcatca                               >  1:788160/2‑70 (MQ=255)
                                        acgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcatca                               >  1:4714803/2‑70 (MQ=255)
                                        acgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcatca                               >  1:2827556/2‑70 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTcgc                                                         <  1:975174/43‑1 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTcgc                                                         <  1:1759731/43‑1 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTcgc                                                         <  1:3769048/43‑1 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGt                                                       >  1:2429850/1‑45 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGt                                                       >  1:2350963/1‑45 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGt                                                       >  1:4551204/1‑45 (MQ=255)
                                         cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaaa                                         >  1:2286834/1‑59 (MQ=255)
                                         cgcAAGCCACTTCACAGGTACGGCAACCGATACAtttc                                                              >  1:653348/1‑37 (MQ=25)
                                         cgcAAGCCACTTCACAGGTACGGCAACCGATACAtttc                                                              >  1:2159770/1‑37 (MQ=25)
                                         cgcAAGCCACTTCACAGGTACGGCAACCGATACAtttc                                                              >  1:4546304/1‑37 (MQ=25)
                                         cgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaacc                                        <  1:1726768/60‑3 (MQ=255)
                                          gcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataataa                                           <  1:3399526/56‑3 (MQ=255)
                                          gcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataataa                                           <  1:2872217/56‑3 (MQ=255)
                                           cACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                           <  1:4459305/71‑1 (MQ=255)
                                            aCGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtc                          <  1:1406533/71‑1 (MQ=255)
                                             cGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAAtgatga                                           <  1:220667/53‑1 (MQ=255)
                                                  cTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                            <  1:1849232/47‑2 (MQ=255)
                                                  cTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaaa                                         >  1:2833369/1‑50 (MQ=255)
                                                  cTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGc                    <  1:4611331/71‑1 (MQ=255)
                                                   ttCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                        <  1:780530/50‑1 (MQ=255)
                                                    tCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaa                                                 >  1:1186528/1‑40 (MQ=255)
                                                     cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACgg                                      >  1:2277003/1‑50 (MQ=255)
                                                     cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACTGTTCATCAAATTCTCCAGCAAt                 >  1:2634725/1‑71 (MQ=255)
                                                     cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCaa                  >  1:761459/1‑70 (MQ=255)
                                                     cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAAt                 >  1:4893344/1‑71 (MQ=255)
                                                     cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAAt                 >  1:3200815/1‑71 (MQ=255)
                                                      acaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCGAGCAAt                 <  1:4551119/70‑1 (MQ=255)
                                                      acaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAAt                 <  1:1570595/70‑1 (MQ=255)
                                                         ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                             >  1:2382824/1‑39 (MQ=255)
                                                         ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                             >  1:2881310/1‑39 (MQ=255)
                                                         ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                             >  1:3002386/1‑39 (MQ=255)
                                                           tACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt           <  1:3427/71‑1 (MQ=255)
                                                            aCGGCAACCAATACATTTACTCGCGTCAGCAAttatga                                           <  1:4235802/38‑1 (MQ=255)
                                                            aCGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt           <  1:3380428/70‑1 (MQ=255)
                                                             cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGtt          <  1:3680/70‑1 (MQ=255)
                                                              ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGAc              <  1:266824/65‑1 (MQ=255)
                                                               gCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa        >  1:3059631/1‑70 (MQ=255)
                                                                  aCCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATgcg    >  1:5187152/1‑71 (MQ=255)
                                                                    cAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCa                   >  1:5682124/1‑54 (MQ=255)
                                                                    cAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGcc  >  1:3609962/1‑71 (MQ=255)
                                                                     |                                                                     
GGTCAGCGATGCACAGTCCTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCC  >  minE/1826216‑1826354

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