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
A4 F21 I0 R1 1009 73.8 4146436 87.4% 3623985 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,073,779 G→A 25.0% G145D (GGT→GAT)  ebgA → cryptic beta‑D‑galactosidase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,073,7790GA25.0% 171.1 / 57.9 92G145D (GGT→GAT) ebgAcryptic beta‑D‑galactosidase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (39/30);  new base A (6/17);  total (45/47)
Fisher's exact test for biased strand distribution p-value = 1.57e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01

GCAGGGTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGATGGTTAAAAC  >  minE/2073714‑2073848
                                                                 |                                                                     
gCAGGGTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAg                                                                   >  1:799841/1‑70 (MQ=255)
  aGGGTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAt                                                                <  1:1936887/71‑1 (MQ=255)
  aGGGTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAt                                                                >  1:3781009/1‑71 (MQ=255)
   gggTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAg                                                                   <  1:3335579/67‑1 (MQ=255)
   gggTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAtg                                                               <  1:3688911/71‑1 (MQ=255)
      tAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAg                                                                   <  1:1106007/64‑1 (MQ=255)
      tAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGTa                                                                 >  1:635693/1‑66 (MQ=255)
      tAAACAGACGATGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAt                                                                >  1:3410647/1‑67 (MQ=255)
       aaaCAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAt                                                                <  1:3648625/66‑1 (MQ=255)
        aaCAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAg                                                                   >  1:3298774/1‑62 (MQ=255)
        aaCAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGt                                                          >  1:977665/1‑71 (MQ=255)
         aCAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAtgtg                                                             <  1:1665595/67‑1 (MQ=255)
          cAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGttt                                                        <  1:1129458/71‑1 (MQ=255)
           aGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAtg                                                               >  1:1308602/1‑63 (MQ=255)
           aGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTc                                                       <  1:2606736/71‑1 (MQ=255)
            gACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGttt                                                        >  1:3759102/1‑69 (MQ=255)
              cGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGc                                                    <  1:133740/71‑1 (MQ=255)
               gCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGt                                                                  <  1:2756289/56‑1 (MQ=255)
               gCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGt                                                                  <  1:3000732/56‑1 (MQ=255)
                  gATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAgg                                                >  1:2516520/1‑71 (MQ=255)
                   aTTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAggg                                               <  1:1667343/71‑1 (MQ=255)
                   aTTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAggg                                               <  1:809310/71‑1 (MQ=255)
                   aTTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGCAAg                                                 <  1:438697/69‑1 (MQ=255)
                   aTTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGCAAg                                                 <  1:2773589/69‑1 (MQ=255)
                    ttAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGt                                                                      <  1:879813/47‑1 (MQ=255)
                    ttAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGt                                                                      <  1:750541/47‑1 (MQ=255)
                    ttAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCa                                                      <  1:1291856/63‑1 (MQ=255)
                     tAAATTTGACGGCGTCGAAACCTTTTTTGAAGTCTATGTTAACgg                                                                       >  1:577127/1‑45 (MQ=255)
                     tAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAggg                                               >  1:2907318/1‑69 (MQ=255)
                      aaaTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCa                                                                    >  1:655127/1‑47 (MQ=255)
                      aaaTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAtg                                                               >  1:1730126/1‑52 (MQ=255)
                      aaaTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAggg                                               >  1:1456931/1‑68 (MQ=255)
                      aaaTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCa                                             <  1:3520690/70‑1 (MQ=255)
                       aaTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAtg                                                               >  1:3846355/1‑51 (MQ=255)
                        aTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTc                                          <  1:875977/71‑1 (MQ=255)
                        aTTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTc                                          >  1:354804/1‑71 (MQ=255)
                           tGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTAt                                                                >  1:1242266/1‑46 (MQ=255)
                            gACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCt                                      >  1:3670950/1‑71 (MQ=255)
                             aCGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTg                                     <  1:1080763/71‑1 (MQ=255)
                                gCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTa                                                                 <  1:798730/40‑1 (MQ=255)
                                gCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTa                                                                 <  1:2061620/40‑1 (MQ=255)
                                 cGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCg                                 <  1:3966116/71‑1 (MQ=255)
                                  gTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAg                                                     <  1:1810537/50‑1 (MQ=255)
                                   tCGAAACCTATTTTGAAGTCTATGTTAACGGTCAg                                                                   <  1:4055952/35‑1 (MQ=255)
                                     gAAACCTATTTTGAAGTCTATGTTAACGGTCAGTa                                                                 >  1:2389224/1‑35 (MQ=255)
                                     gAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCa                               >  1:4100397/1‑69 (MQ=255)
                                     gAAACCTATTTTGAAGTCTATGTTAACGATCAGTa                                                                 >  1:3895101/1‑35 (MQ=255)
                                     gAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGc                                                    <  1:3474660/48‑1 (MQ=255)
                                     gAAACCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGc                                                    <  1:1575263/48‑1 (MQ=255)
                                      aaaCCTATTTTGAAGTCTATGTTAACGGTGAGTATGGGGGTTTCAGCAAGGGCAGTCGCCTGACCGCag                              <  1:2469870/69‑1 (MQ=255)
                                       aaCCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGt                           >  1:1324220/1‑71 (MQ=255)
                                        aCCTATTTTGAAGTCTATGTTAACGGTCAGTAtgtg                                                             >  1:2441102/1‑36 (MQ=255)
                                        aCCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAg                                                 <  1:2010394/48‑1 (MQ=255)
                                        aCCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCa                                             >  1:832875/1‑52 (MQ=255)
                                        aCCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCa                                             >  1:1320417/1‑52 (MQ=255)
                                        aCCTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGtt                          >  1:2050634/1‑71 (MQ=255)
                                         ccTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGttt                         <  1:669482/71‑1 (MQ=255)
                                         ccTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGttt                         <  1:365954/71‑1 (MQ=255)
                                          cTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAggg                                               >  1:201451/1‑48 (MQ=255)
                                          cTATTTTGAAGTCTATGTTAACGATCAGTATGTGGGTTTc                                                       <  1:2535414/40‑1 (MQ=255)
                                             ttttGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAg                                            >  1:2558705/1‑48 (MQ=255)
                                             ttttGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAg                                            >  1:1219596/1‑48 (MQ=255)
                                             ttttGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTc                                          <  1:195555/50‑1 (MQ=255)
                                              tttGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACAt                    >  1:3952745/1‑71 (MQ=255)
                                               ttGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGa                                    >  1:1027761/1‑54 (MQ=255)
                                               ttGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACAt                    >  1:1647196/1‑70 (MQ=255)
                                                 gAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAg                                                     <  1:1817157/35‑1 (MQ=255)
                                                 gAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAg                 >  1:981851/1‑71 (MQ=255)
                                                 gAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAg                 >  1:2386731/1‑71 (MQ=255)
                                                  aaGTCTATGTTAACGGTCAGTATGTGGGTTTCAGc                                                    <  1:3888335/35‑1 (MQ=255)
                                                  aaGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCa                                             <  1:2977349/42‑1 (MQ=255)
                                                  aaGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCa                                             <  1:708033/42‑1 (MQ=255)
                                                  aaGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGtt                          <  1:2845791/61‑1 (MQ=255)
                                                    gTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGttt                         >  1:3877553/1‑60 (MQ=255)
                                                     tCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCg                                         >  1:69095/1‑43 (MQ=255)
                                                     tCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGc                                        >  1:2866868/1‑44 (MQ=255)
                                                     tCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGc                                        >  1:2366753/1‑44 (MQ=255)
                                                     tCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCagag                            <  1:2337974/56‑1 (MQ=255)
                                                     tCTATGTTAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCa                               <  1:451110/53‑1 (MQ=255)
                                                       tATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTc                                          >  1:951360/1‑40 (MQ=255)
                                                       tATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGc                                        >  1:2824941/1‑42 (MQ=255)
                                                       tATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCa                               >  1:445752/1‑51 (MQ=255)
                                                       tATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCa                               >  1:2692909/1‑51 (MQ=255)
                                                       tATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCa                               >  1:3554423/1‑51 (MQ=255)
                                                       tATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGa                       >  1:1948605/1‑59 (MQ=255)
                                                         tGTTAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAgc                <  1:670113/64‑1 (MQ=255)
                                                         tGTTAACGACCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAgc                <  1:1025126/64‑1 (MQ=255)
                                                           ttAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGa            <  1:2352063/66‑1 (MQ=255)
                                                           ttAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGATGGt        <  1:2884832/70‑1 (MQ=255)
                                                           ttAACGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGATGGt        <  1:488830/70‑1 (MQ=255)
                                                             aaCGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGtt                          >  1:3658234/1‑50 (MQ=255)
                                                             aaCGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGATGGTTa      <  1:783272/70‑1 (MQ=255)
                                                             aaCGATCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGttt                         >  1:3811756/1‑51 (MQ=255)
                                                                ggTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGATGGTTAAAAc  <  1:409039/71‑1 (MQ=255)
                                                                 |                                                                     
GCAGGGTAAACAGACGCTGATTAAATTTGACGGCGTCGAAACCTATTTTGAAGTCTATGTTAACGGTCAGTATGTGGGTTTCAGCAAGGGCAGTCGCCTGACCGCAGAGTTTGACATCAGCGCGATGGTTAAAAC  >  minE/2073714‑2073848

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