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 1,826,303 A→C 21.5% A7A (GCT→GCG)  hydN ← formate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,826,3030AC21.5% 204.4 / 78.5 130A7A (GCT→GCG) hydNformate dehydrogenase‑H, [4Fe‑4S] ferredoxin subunit
Reads supporting (aligned to +/- strand):  ref base A (54/48);  new base C (13/15);  total (67/63)
Fisher's exact test for biased strand distribution p-value = 6.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

Only 100 of 130 total aligned reads displayed.

CTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTCACA  >  minE/1826234‑1826366
                                                                     |                                                               
cTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                                >  1:880577/1‑71 (MQ=255)
cTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                                >  1:4335482/1‑71 (MQ=255)
cTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                                >  1:3502090/1‑71 (MQ=255)
  gATTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGc                                                               >  1:5298515/1‑70 (MQ=255)
  gATTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGc                                                               >  1:4850430/1‑70 (MQ=255)
   aTTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCaa                                                             >  1:5036326/1‑71 (MQ=255)
   aTTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCa                                                              <  1:2285167/70‑1 (MQ=255)
   aTTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGc                                                               <  1:602642/69‑1 (MQ=255)
   aTTTTCCTGATGAGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGc                                                               <  1:1264433/69‑1 (MQ=255)
   aTTCTCATGATGCGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGc                                                               <  1:3267245/69‑1 (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                                                     >  1:1356230/1‑70 (MQ=255)
           gatgcGACACTGCGCAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaac                                                     >  1:3092677/1‑70 (MQ=255)
            atgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                                    >  1:860411/1‑71 (MQ=255)
            atgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                                    >  1:5350741/1‑71 (MQ=255)
            atgaGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                                    >  1:2564220/1‑71 (MQ=255)
            atgaGAAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAAc                                                    >  1:4810690/1‑71 (MQ=255)
             tgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACg                                                   >  1:1061345/1‑71 (MQ=255)
             tgaGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACg                                                   >  1:3193442/1‑71 (MQ=255)
              gagaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:4546756/1‑64 (MQ=255)
              gagaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACgg                                                  >  1:4285982/1‑71 (MQ=255)
               agaAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                                 >  1:4197328/1‑71 (MQ=255)
                gaAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGt                                                 >  1:3715697/1‑70 (MQ=255)
                gaAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaa                                                      >  1:113282/1‑65 (MQ=255)
                gaAACCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGtt                                                <  1:4195368/71‑1 (MQ=255)
                 aaaCCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtc                                               <  1:1646897/71‑1 (MQ=255)
                 aaaCCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAg                                                                <  1:5528802/54‑1 (MQ=255)
                   actgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcat                                             <  1:846580/68‑1 (MQ=255)
                   actgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcat                                             >  1:1878049/4‑71 (MQ=255)
                   aCCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCa                                                              >  1:3727298/1‑54 (MQ=255)
                   aCCACGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCa                                                              >  1:1485272/1‑54 (MQ=255)
                    ctgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatg                                            <  1:363866/69‑2 (MQ=255)
                    ctgcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATAAACCGGTtcatg                                            <  1:437939/69‑2 (MQ=255)
                      gcgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                                        >  1:685906/1‑56 (MQ=255)
                      gcgcAAGCCACTTCACAGGTACGGCAACCGATACAATTCGTCGCATCCGCAATAATAAACCgg                                                  >  1:2367061/1‑63 (MQ=255)
                      acgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcatca                                           >  1:4714803/2‑70 (MQ=255)
                      acgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcatca                                           >  1:788160/2‑70 (MQ=255)
                      acgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTtcatca                                           >  1:2827556/2‑70 (MQ=255)
                      acgcACGCTACTTCACAGGTACGGCAACCAATACAATTACTCCCGTCAGCa                                                              >  1:1079576/2‑51 (MQ=255)
                       cgcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaaa                                                     >  1:2286834/1‑59 (MQ=255)
                       cgcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCAATAATaaacc                                                    <  1:1726768/60‑3 (MQ=255)
                        gcACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAatgatg                                                        <  1:227899/55‑1 (MQ=255)
                        gcAAGCCACTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataataa                                                       <  1:3399526/56‑3 (MQ=255)
                         cACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                                       <  1:3055557/71‑1 (MQ=255)
                         cACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                                       <  1:4459305/71‑1 (MQ=255)
                          aCGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtc                                      <  1:4349942/71‑1 (MQ=255)
                            gCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtct                                     >  1:4964328/1‑70 (MQ=255)
                              tACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                                       >  1:2931810/1‑66 (MQ=255)
                                cTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                                        <  1:683848/47‑2 (MQ=255)
                                cTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                                        <  1:1849232/47‑2 (MQ=255)
                                cTTCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaataata                                                        <  1:3698722/47‑2 (MQ=255)
                                cTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGaaa                                                     >  1:2833369/1‑50 (MQ=255)
                                cTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGc                                <  1:4611331/71‑1 (MQ=255)
                                  tCACAGGTACGGCAACCGATACATTTCGTCGCATCCGCaa                                                             >  1:1485004/1‑40 (MQ=255)
                                  tCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCaa                              >  1:875849/1‑71 (MQ=255)
                                   cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACgg                                                  >  1:1649699/1‑50 (MQ=255)
                                   cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACgg                                                  >  1:2277003/1‑50 (MQ=255)
                                   cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACTGTTCATCAAATTCTCCAGCAAt                             >  1:2634725/1‑71 (MQ=255)
                                   cacaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCaa                              >  1:761459/1‑70 (MQ=255)
                                    acaGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAAt                             <  1:1570595/70‑1 (MQ=255)
                                      aGGTACGGCAACCGATACATTTCGTCGCATCCGCAat                                                            >  1:2481015/1‑37 (MQ=16)
                                       ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:2881310/1‑39 (MQ=255)
                                       ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:3002386/1‑39 (MQ=255)
                                       ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:2382824/1‑39 (MQ=255)
                                       ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:4438090/1‑39 (MQ=255)
                                       ggTACGGCAACCAATACATTTACTCGCGTCAGCAatgat                                                         >  1:4887213/1‑39 (MQ=255)
                                         tACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       <  1:3427/71‑1 (MQ=255)
                                          aCGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       <  1:3380428/70‑1 (MQ=255)
                                           cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGtt                      <  1:3680/70‑1 (MQ=255)
                                           cGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGtt                      <  1:2694846/70‑1 (MQ=255)
                                            ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGAc                          <  1:2180224/65‑1 (MQ=255)
                                            ggCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGAc                          <  1:2658611/65‑1 (MQ=255)
                                             gCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa                    >  1:3059631/1‑70 (MQ=255)
                                                aCCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATgcg                >  1:5187152/1‑71 (MQ=255)
                                                  cAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGcc              >  1:3609962/1‑71 (MQ=255)
                                                    aTACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGt                       <  1:4153070/60‑1 (MQ=255)
                                                    aTACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGa            >  1:533537/1‑71 (MQ=255)
                                                     tACATTTACTCGCGTCAGCAATGATGAAACGGTTAATCAAATtc                                      <  1:379588/44‑1 (MQ=255)
                                                      aCATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATa          >  1:3074050/1‑71 (MQ=255)
                                                       cATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATtct                                     >  1:5587444/1‑43 (MQ=255)
                                                       cATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTcc                                   >  1:2136589/1‑45 (MQ=255)
                                                        aTTTACTCGCGTCAGCAATGATGAAACGGTTCATCaaa                                         <  1:3890578/38‑1 (MQ=255)
                                                          ttACTCGCGTCAGCAATGATGAAACGGTTCATCAAAtt                                       >  1:3844548/1‑38 (MQ=255)
                                                          ttACTCGCGTCAGCAATGATGAAACGGTTCATCAAAt                                        >  1:4324407/1‑37 (MQ=255)
                                                          ttACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACAtt      >  1:1775688/1‑71 (MQ=255)
                                                             cTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGc                                <  1:980644/42‑1 (MQ=255)
                                                             cTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGc                                <  1:3270990/42‑1 (MQ=255)
                                                              tCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa                    <  1:1984563/53‑1 (MQ=255)
                                                               cgcgTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa                    <  1:3071083/52‑1 (MQ=255)
                                                                gcgTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTcaca  <  1:3063555/69‑1 (MQ=255)
                                                                gcgTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTcaca  <  1:3651172/69‑1 (MQ=255)
                                                                gcgTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTcaca  <  1:4505748/69‑1 (MQ=255)
                                                                   tCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCa                               <  1:1916927/37‑1 (MQ=255)
                                                                   tCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTaa                    <  1:5405472/48‑1 (MQ=255)
                                                                   tCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGcc              <  1:1102610/54‑1 (MQ=255)
                                                                   tCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGcc              <  1:4544233/54‑1 (MQ=255)
                                                                   tCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATa          <  1:1397349/58‑1 (MQ=255)
                                                                     |                                                               
CTGATTTTCCTGATGAGAAACCGCGCACGCTACTTCACAGGTACGGCAACCAATACATTTACTCGCGTCAGCAATGATGAAACGGTTCATCAAATTCTCCAGCAATGACAGTTAATGCGCCGATACATTCACA  >  minE/1826234‑1826366

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