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 218,157 C→T 22.8% D48D (GAC→GAT)  yafF → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported218,1570CT22.8% 305.2 / 84.2 162D48D (GAC→GAT) yafFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (67/58);  new base T (18/19);  total (85/77)
Fisher's exact test for biased strand distribution p-value = 7.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

Only 100 of 164 total aligned reads displayed.

AATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGT  >  Exported/218089‑218223
                                                                    |                                                                  
aaTATTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACa                                                                   <  1:5304034/70‑1 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 <  1:3503476/70‑1 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 >  1:2251442/1‑70 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 <  1:4680091/70‑1 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 >  1:4715980/1‑70 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 <  1:5140282/70‑1 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 <  1:1887636/70‑1 (MQ=255)
  tatTTTGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 <  1:3470379/70‑1 (MQ=255)
  tatTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGa                                                                 <  1:2102764/70‑1 (MQ=255)
    ttttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaa                                                                <  1:3282201/69‑1 (MQ=255)
    ttttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaa                                                                <  1:1509462/69‑1 (MQ=255)
    ttttGACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAAc                                                              >  1:5523771/1‑71 (MQ=255)
    ttttAACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGaa                                                                <  1:2770489/69‑1 (MQ=255)
      ttaaCGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACt                                                             <  1:2379544/67‑1 (MQ=255)
        gACGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACa                                                                   <  1:4241833/62‑1 (MQ=255)
         aCGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCt                                                         <  1:4838807/71‑1 (MQ=255)
              tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCt                                                         <  1:5416401/66‑1 (MQ=255)
                ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGATAAGCAGCCATGGACAGaa                                                                >  1:17552/3‑57 (MQ=255)
                ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaaa                                                               >  1:5087652/3‑58 (MQ=255)
                ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaaa                                                               >  1:4960252/3‑58 (MQ=255)
                ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaa                                                                >  1:3927575/3‑57 (MQ=255)
                ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTc                                                   <  1:3974561/68‑1 (MQ=255)
                ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGt                                                    >  1:3304418/3‑69 (MQ=255)
                 taaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAg                                                 >  1:5249375/2‑71 (MQ=255)
                  aaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGa                                                                 <  1:2392675/54‑1 (MQ=255)
                  aaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                 >  1:3483338/1‑70 (MQ=255)
                   aGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                <  1:4680723/70‑1 (MQ=255)
                    ggTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTcc                                              <  1:3881365/71‑1 (MQ=255)
                     gTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCt                                             <  1:3867706/71‑1 (MQ=255)
                      tATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCtt                                            <  1:2451934/71‑1 (MQ=255)
                        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACt                                                             <  1:2998032/52‑1 (MQ=255)
                        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACt                                                             <  1:4926133/52‑1 (MQ=255)
                        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATTTGGCGTCAGTCCTTGc                                          <  1:1664669/71‑1 (MQ=255)
                        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                 <  1:531635/64‑1 (MQ=255)
                        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                 <  1:1008257/64‑1 (MQ=255)
                        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCtta                                           <  1:1008818/70‑2 (MQ=255)
                         tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCg                                         >  1:5050505/1‑71 (MQ=255)
                          cAAGGCATGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgg                                        >  1:2166309/1‑71 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCgg                                        >  1:4845463/1‑71 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCgg                                        >  1:792673/1‑71 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                  >  1:1116609/1‑61 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                  >  1:3382194/1‑61 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCttac                                          >  1:5580842/1‑67 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:3109827/1‑71 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:2598466/1‑71 (MQ=255)
                          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:380270/1‑71 (MQ=255)
                           aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAAc                                                              >  1:3521461/1‑48 (MQ=255)
                           aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCgg                                        <  1:5237182/70‑1 (MQ=255)
                           aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgg                                        >  1:2833266/1‑70 (MQ=255)
                             ggCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGa                                     <  1:4380476/71‑1 (MQ=255)
                                aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaaa                                                               >  1:2302272/1‑42 (MQ=255)
                                 gggTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCgg                                 >  1:3965276/1‑71 (MQ=255)
                                   gTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCgggg                                      <  1:5216980/64‑1 (MQ=255)
                                    ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaaa                                                               >  1:3265805/1‑38 (MQ=255)
                                    ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGaaa                                                               >  1:2721919/1‑38 (MQ=255)
                                    ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCt                              >  1:3987943/1‑71 (MQ=255)
                                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                  >  1:4586445/1‑49 (MQ=255)
                                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCttt                            >  1:899542/1‑71 (MQ=255)
                                        gACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCGGGCTTTCg                          <  1:1388404/71‑1 (MQ=255)
                                          cGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGc                                          >  1:745403/1‑53 (MQ=255)
                                          cGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgta                        <  1:2202383/71‑1 (MQ=255)
                                          cGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgta                        <  1:1786494/71‑1 (MQ=255)
                                           gTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGt                                                    >  1:2020530/1‑42 (MQ=255)
                                            tAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCg                                         <  1:664308/52‑1 (MQ=255)
                                            tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtag                       >  1:1978372/1‑70 (MQ=255)
                                            tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgggg                                      <  1:3460643/55‑1 (MQ=255)
                                             aaGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCGGGCTTTc                           >  1:2716047/1‑65 (MQ=255)
                                             aaGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGAGGGGAGCGGGCTTTc                           >  1:4938711/1‑65 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCa                                                  <  1:5604824/40‑1 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCa                                                  <  1:1311927/40‑1 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                               <  1:3547129/43‑1 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                               <  1:2275215/43‑1 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                               <  1:5034668/43‑1 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                               <  1:1664192/43‑1 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                  >  1:5440118/1‑40 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                  >  1:2913806/1‑40 (MQ=255)
                                               gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                  >  1:4168556/1‑40 (MQ=255)
                                               gATGCGAAAAGCAGCCATCGACAGAAACTACCTGGCGTc                                                   >  1:1177256/1‑39 (MQ=255)
                                                aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                         <  1:2830334/48‑1 (MQ=255)
                                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                >  1:2245327/1‑37 (MQ=37)
                                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                >  1:3451041/1‑37 (MQ=37)
                                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                >  1:3422703/1‑37 (MQ=37)
                                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                >  1:3020164/1‑37 (MQ=37)
                                                    gAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtagta                     >  1:654207/1‑64 (MQ=255)
                                                     aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:3709748/1‑44 (MQ=255)
                                                     aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:3008033/1‑44 (MQ=255)
                                                     aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:3215063/1‑44 (MQ=255)
                                                       aaGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCggg                                       <  1:4944522/43‑1 (MQ=255)
                                                       aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                        >  1:640366/1‑42 (MQ=255)
                                                       aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCg                                  >  1:1994317/1‑48 (MQ=255)
                                                       aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCtt                             <  1:418260/53‑1 (MQ=255)
                                                         gcagcCATGGACAGAAACTACCTGGCGTCAGTCCTTGCg                                         <  1:4232697/39‑1 (MQ=255)
                                                         gcagcCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTc                           >  1:454470/1‑53 (MQ=255)
                                                             ccATGGACAGAAACTATCTGGCGTCAGTCCTTGCgg                                        <  1:1481279/36‑1 (MQ=255)
                                                                tGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtaa                       <  1:1025200/50‑2 (MQ=255)
                                                                  gACAGAAACTACCTGGCGTCAGTCCTTACGGGGAg                                    >  1:5442247/1‑35 (MQ=255)
                                                                   aCAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtaa                       >  1:588114/1‑46 (MQ=255)
                                                                   aCAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCgtaat                      <  1:1560499/48‑3 (MQ=39)
                                                                    cAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCttt                            >  1:4446192/1‑41 (MQ=255)
                                                                    cAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGAct          >  1:1316173/1‑59 (MQ=255)
                                                                    |                                                                  
AATATTTTGACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGT  >  Exported/218089‑218223

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