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 218,166 C→T 44.0% Y51Y (TAC→TAT)  yafF → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported218,1660CT44.0% 54.7 / 157.5 135Y51Y (TAC→TAT) yafFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (48/27);  new base T (28/31);  total (76/59)
Fisher's exact test for biased strand distribution p-value = 7.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

Only 100 of 136 total aligned reads displayed.

ACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTA  >  Exported/218098‑218228
                                                                    |                                                              
aCGAATGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCt                                                              <  1:1550875/71‑1 (MQ=255)
   aaTGATTAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTAc                                                                <  1:530903/66‑1 (MQ=255)
     tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCt                                                              <  1:5416401/66‑1 (MQ=255)
     tGATAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCt                                                              <  1:4857886/66‑1 (MQ=255)
       ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTc                                                        <  1:3974561/68‑1 (MQ=255)
       ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGt                                                         >  1:3304418/3‑69 (MQ=255)
       ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGt                                                         >  1:4955145/3‑69 (MQ=255)
        taaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAg                                                      >  1:5249375/2‑71 (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)
               ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                      <  1:1008257/64‑1 (MQ=255)
               ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCtta                                                <  1:1008818/70‑2 (MQ=255)
                tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGt                                                         <  1:592374/60‑1 (MQ=255)
                tCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCg                                              >  1:5050505/1‑71 (MQ=255)
                 cAAGGCATGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgg                                             >  1:2166309/1‑71 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCgg                                             >  1:4845463/1‑71 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCg                                              <  1:1015791/70‑1 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:3382194/1‑61 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:1116609/1‑61 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCttac                                               >  1:5580842/1‑67 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:1789837/1‑71 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:3109827/1‑71 (MQ=255)
                 cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:1346359/1‑71 (MQ=255)
                  aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:1717743/1‑60 (MQ=255)
                  aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgg                                             >  1:2833266/1‑70 (MQ=255)
                       aGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                              >  1:1944452/1‑64 (MQ=255)
                        gggTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCgg                                      >  1:3965276/1‑71 (MQ=255)
                          gTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCgggg                                           <  1:5216980/64‑1 (MQ=255)
                           ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCggg                                            <  1:710175/62‑1 (MQ=255)
                           ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGc                                    >  1:3009295/1‑70 (MQ=255)
                           ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCt                                   >  1:3987943/1‑71 (MQ=255)
                           ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGt                                                         <  1:1603909/49‑1 (MQ=255)
                           ttAAGACGTAAGATGCGAAAAGAAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCggg                                            <  1:3304238/62‑1 (MQ=255)
                             aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCtt                                  <  1:2727779/70‑1 (MQ=255)
                             aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:4586445/1‑49 (MQ=255)
                             aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTg                                                >  1:852468/1‑56 (MQ=255)
                             aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTg                                                >  1:1125942/1‑56 (MQ=255)
                             aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCttt                                 >  1:899542/1‑71 (MQ=255)
                               gACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCg                               >  1:3774724/1‑71 (MQ=255)
                                aCGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTGGCGGGGAGCGGGCTTTCgt                              <  1:3962684/71‑1 (MQ=255)
                                aCGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgt                              <  1:5643780/71‑1 (MQ=255)
                                 cGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGc                                               >  1:745403/1‑53 (MQ=255)
                                 cGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgta                             <  1:1786494/71‑1 (MQ=255)
                                  gTAAGATGCGAAAAGCAGCCATTGATAGAAACTATCTCGCGt                                                         >  1:468321/1‑42 (MQ=255)
                                  gTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGt                                                         >  1:2020530/1‑42 (MQ=255)
                                  gTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtaa                            >  1:4585127/1‑70 (MQ=255)
                                   tAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCg                                              <  1:664308/52‑1 (MQ=255)
                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtaa                            <  1:4927959/70‑2 (MQ=255)
                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtag                            >  1:1978372/1‑70 (MQ=255)
                                   tAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACgggg                                           <  1:3460643/55‑1 (MQ=255)
                                    aaGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCGGGCTTTc                                >  1:2716047/1‑65 (MQ=255)
                                    aaGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCGGGGAGCGGGCTTTc                                >  1:4112011/1‑65 (MQ=255)
                                    aaGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgta                             >  1:3841719/1‑68 (MQ=255)
                                     aGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCggg                                            >  1:3489218/1‑52 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCa                                                       <  1:5604824/40‑1 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCa                                                       <  1:1311927/40‑1 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:1664192/43‑1 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:2275215/43‑1 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:4400580/43‑1 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:5034668/43‑1 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:2913806/1‑40 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:5440118/1‑40 (MQ=255)
                                      gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTc                                >  1:2241696/1‑63 (MQ=255)
                                      gATGCGAAAAGCAGCCATCGACAGAAACTACCTGGCGTc                                                        >  1:1177256/1‑39 (MQ=255)
                                       aTGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCg                               >  1:5043737/1‑63 (MQ=255)
                                       aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                              <  1:2024620/48‑1 (MQ=255)
                                       aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                              <  1:312583/48‑1 (MQ=255)
                                       aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                              <  1:2830334/48‑1 (MQ=255)
                                           gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:2245327/1‑37 (MQ=37)
                                           gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:3422703/1‑37 (MQ=37)
                                           gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:5230840/1‑37 (MQ=37)
                                           gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:3451041/1‑37 (MQ=37)
                                           gAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtagta                          >  1:654207/1‑64 (MQ=255)
                                           gAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATAcccc                   <  1:22903/71‑1 (MQ=255)
                                            aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:3709748/1‑44 (MQ=255)
                                            aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:3008033/1‑44 (MQ=255)
                                            aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:4200298/1‑44 (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)
                                                       tGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGt       <  1:32265/71‑1 (MQ=255)
                                                         gACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCg                                       >  1:5167082/1‑37 (MQ=255)
                                                         gACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGa                 <  1:269346/59‑1 (MQ=255)
                                                         gACAGAAACTACCTGGCGTCAGTCCTTACGGGGAg                                         >  1:5442247/1‑35 (MQ=255)
                                                         gACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCgtaat                           >  1:4749352/1‑47 (MQ=39)
                                                           taGAAACTAGCTGACGTAAGTCCTTGCGGGGAGCAGGGTTTCgta                             <  1:4048999/44‑1 (MQ=255)
                                                           cAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCttt                                 >  1:4446192/1‑41 (MQ=255)
                                                           cAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGAct               >  1:1316173/1‑59 (MQ=255)
                                                            aGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATTCCCCGCCTCTcccc         >  1:2861394/1‑64 (MQ=255)
                                                            aGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTc                                >  1:5542994/1‑41 (MQ=255)
                                                             gAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCtt                                  <  1:5284256/38‑1 (MQ=255)
                                                                  tACCTGACGTCAGTCCTTGCGGGGAGCAGGCTTTCgtaaa                           <  1:1559698/40‑3 (MQ=255)
                                                                   aCCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTaa                         <  1:5487540/41‑1 (MQ=255)
                                                                    |                                                              
ACGAATGAGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTA  >  Exported/218098‑218228

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