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
A3 F2 I1 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 Exported 218,106 G→T 82.3% E31D (GAG→GAT)  yafF → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported218,1060GT82.3% 486.2 / 125.4 260E31D (GAG→GAT) yafFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (16/30);  new base T (97/117);  total (113/147)
Fisher's exact test for biased strand distribution p-value = 2.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 268 total aligned reads displayed.

GAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCT  >  Exported/218039‑218168
                                                                   |                                                              
 aagaGGAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAgg                                                            <  1:5116099/71‑1 (MQ=255)
   gagGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAgg                                                            <  1:3475987/69‑1 (MQ=255)
      gAAATGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTAtt                                                        >  1:4751481/1‑70 (MQ=255)
       aaaTGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTc                                                       >  1:2406640/1‑70 (MQ=255)
       aaaTGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTc                                                       >  1:1071531/1‑70 (MQ=255)
          cGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAgg                                                   >  1:1425078/1‑71 (MQ=255)
           gccgcagAATTATTTTCAGGGATACGGCACATCGCTATTAATATTTTAACGAATGATAAGGTATTCAAgg                                                   >  1:1937179/4‑70 (MQ=255)
               cagAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATgag                                                                <  1:212942/53‑1 (MQ=255)
                 gAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGtt                                            <  1:3676977/71‑1 (MQ=255)
                 gAATTATTTTAAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGtt                                            <  1:2445970/71‑1 (MQ=255)
                  aaTTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGc                                                  <  1:3392236/64‑1 (MQ=255)
                   attattTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTaa                                          <  1:4538674/71‑1 (MQ=255)
                   attattTTCAGGGATACGGCACATCGCTATTAATATTTTAACGAATGATAAGGTAt                                                         >  1:2995486/1‑56 (MQ=255)
                    ttattTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCaa                                                     >  1:4741635/1‑59 (MQ=255)
                    ttattTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGtt                                            >  1:4591122/1‑68 (MQ=255)
                     tattTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGa                                        >  1:1265587/1‑71 (MQ=255)
                      attTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGAc                                       >  1:4119912/1‑71 (MQ=255)
                      attTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGAc                                       >  1:4511087/1‑71 (MQ=255)
                      attTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGAc                                       >  1:1150421/1‑71 (MQ=255)
                       ttttCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGAc                                       >  1:3702722/1‑70 (MQ=255)
                       ttttCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACg                                      <  1:553899/71‑1 (MQ=255)
                       ttttCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAgg                                                   <  1:1883256/58‑1 (MQ=255)
                       ttttCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAgg                                                   <  1:3086730/58‑1 (MQ=255)
                       ttttCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAgg                                                   <  1:2389882/58‑1 (MQ=255)
                         ttCAGGGATACGGCACATCGCTATTAATATTTTAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGt                                     <  1:3501800/70‑1 (MQ=255)
                              ggATACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTc                                                       <  1:1076976/47‑1 (MQ=255)
                                aTACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGc                              >  1:1540598/1‑70 (MQ=255)
                                aTACGGCACATCGCTATTAATATTTTAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGc                              >  1:4872287/1‑70 (MQ=255)
                                 tACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGt                                             <  1:4252661/54‑1 (MQ=255)
                                 tACGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGAc                                       <  1:2768860/60‑1 (MQ=255)
                                 tACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGa                            <  1:1567104/71‑1 (MQ=255)
                                 tACGGCACATCGCTATTAATATTTTAACGAATGATAAg                                                             <  1:1753269/38‑1 (MQ=37)
                                  aCGGCACATTGCTATTAATATTTTGACGAATGATaa                                                              >  1:3605128/1‑36 (MQ=255)
                                  aCGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGa                            >  1:5064653/1‑70 (MQ=255)
                                  aCGGCACATCGCTATTAATATTTTAACGAATGATAAg                                                             >  1:897682/1‑37 (MQ=37)
                                   cGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCa                                                      >  1:5556179/1‑43 (MQ=255)
                                   cGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGc                                                  <  1:471468/47‑1 (MQ=255)
                                   cGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGaaa                          <  1:2475371/71‑1 (MQ=255)
                                   cGGCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGaa                           <  1:1676918/70‑1 (MQ=255)
                                    ggCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGtt                                            <  1:4718776/52‑1 (MQ=255)
                                     gCACATTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAag                        <  1:2306851/71‑1 (MQ=255)
                                         aTTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTaa                                   <  1:823319/56‑1 (MQ=255)
                                         aTTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAag                        <  1:4191737/67‑1 (MQ=255)
                                         aTTGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAag                        <  1:724639/67‑1 (MQ=255)
                                         aTTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGt                                     <  1:4618368/54‑1 (MQ=255)
                                          ttGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGa                            >  1:5177139/1‑62 (MQ=255)
                                          ttGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAagcagc                    >  1:2714515/1‑70 (MQ=255)
                                          ttGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAagcagc                    >  1:1312504/1‑70 (MQ=255)
                                          ttGCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAagcagc                    >  1:1639338/1‑70 (MQ=255)
                                           tGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCa                  >  1:5341089/1‑71 (MQ=255)
                                           cgCTATTAATATTTTAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCa                  >  1:2160613/2‑71 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCaa                                                     >  1:3295413/1‑35 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGa                                 >  1:4439111/1‑55 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGa                                 >  1:588326/1‑55 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCa                  <  1:5459901/70‑1 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCAt                 >  1:1272297/1‑71 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCAt                 >  1:4572765/1‑71 (MQ=255)
                                            gCTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCAt                 >  1:870558/1‑71 (MQ=255)
                                            gCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCa                  <  1:3770252/70‑1 (MQ=255)
                                             cTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCAt                 <  1:4655726/70‑1 (MQ=255)
                                             cTATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATg                <  1:405282/71‑1 (MQ=255)
                                              tATTAATATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATg                <  1:4421469/70‑1 (MQ=255)
                                               aTTAATATTTTTACGAATGAGAAGGTATTCAAGGCAGGGTTAAg                                         <  1:2085583/44‑1 (MQ=255)
                                               aTTAATATTTTGACGAATGAGAAGGTATTCAAGGCAg                                                <  1:3592985/37‑1 (MQ=255)
                                                ttAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTaa                                   <  1:198751/49‑1 (MQ=255)
                                                ttAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATgg               <  1:490659/69‑1 (MQ=255)
                                                 tAATATTTTAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTaa                                   >  1:4381674/1‑48 (MQ=255)
                                                 tAATATTTTAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTaa                                   >  1:1953704/1‑48 (MQ=255)
                                                  aaTATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGa                                        >  1:5088539/1‑42 (MQ=255)
                                                  aaTATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGTCGTAAGATGCGAAAagcagc                    >  1:1517234/1‑62 (MQ=255)
                                                  aaTATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTaa                                   >  1:3095049/1‑47 (MQ=255)
                                                  aaTATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAagca                      >  1:2618110/1‑60 (MQ=255)
                                                  aaTATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACa            <  1:5304034/70‑1 (MQ=255)
                                                  aaTATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAg                                         <  1:4197259/41‑1 (MQ=255)
                                                  aaTATTTTAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGa                                 >  1:931547/1‑49 (MQ=255)
                                                    tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTaa                                   <  1:3997142/45‑1 (MQ=255)
                                                    tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAg                                  >  1:4905608/1‑46 (MQ=255)
                                                    tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa          <  1:1887636/70‑1 (MQ=255)
                                                    tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa          >  1:2251442/1‑70 (MQ=255)
                                                    tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa          <  1:5140282/70‑1 (MQ=255)
                                                    tatTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAagcagc                    <  1:2861242/60‑1 (MQ=255)
                                                    tatTTTAACGAATGATAAGGTATTCAAGGCAGGGTTaa                                          <  1:320864/38‑1 (MQ=38)
                                                      ttttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGaa                           <  1:2682839/51‑1 (MQ=255)
                                                      ttttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaa         <  1:3282201/69‑1 (MQ=255)
                                                      ttttAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACg                                      <  1:1505664/40‑1 (MQ=255)
                                                       tttAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCAt                 <  1:2938737/60‑1 (MQ=255)
                                                        ttaaCGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACt      <  1:2379544/67‑1 (MQ=255)
                                                        ttaaCGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTa     >  1:2987804/4‑71 (MQ=255)
                                                          gACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAagcag                     <  1:5605300/53‑1 (MQ=255)
                                                           aCGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCt  <  1:4838807/71‑1 (MQ=255)
                                                              aaTGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGAt                                <  1:5235276/38‑1 (MQ=255)
                                                              aaTGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGc                              <  1:1375362/40‑1 (MQ=255)
                                                                tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGaaa                          <  1:3064711/42‑1 (MQ=255)
                                                                tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATg                <  1:3015676/52‑1 (MQ=255)
                                                                tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATg                <  1:3461271/52‑1 (MQ=255)
                                                                tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATg                <  1:3902608/52‑1 (MQ=255)
                                                                tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCt  <  1:5416401/66‑1 (MQ=255)
                                                                tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCt  <  1:4857886/66‑1 (MQ=255)
                                                                 gagaAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGcc                   <  1:5646242/48‑1 (MQ=255)
                                                                  agaAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCAt                 <  1:3568810/49‑1 (MQ=255)
                                                                   |                                                              
GAAGAGGAAACGCAGCAGAATTATTTTCAGGGATACGGCACATTGCTATTAATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCT  >  Exported/218039‑218168

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