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 218,169 G→C 23.4% L52L (CTG→CTC)  yafF → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported218,1690GC23.4% 237.7 / 72.4 130L52L (CTG→CTC) yafFconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (58/41);  new base C (16/14);  total (75/55)
Fisher's exact test for biased strand distribution p-value = 6.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

Only 100 of 134 total aligned reads displayed.

AGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTA  >  Exported/218105‑218228
                                                                |                                                           
ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTc                                                        <  1:3974561/68‑1 (MQ=255)
ataaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGt                                                         >  1:4955145/3‑69 (MQ=255)
  aaGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                      >  1:3483338/1‑70 (MQ=255)
   aGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     <  1:4680723/70‑1 (MQ=255)
   aGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGt                                                     >  1:3987554/1‑70 (MQ=255)
    ggTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTcc                                                   <  1:3881365/71‑1 (MQ=255)
      tATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCtt                                                 <  1:2451934/71‑1 (MQ=255)
        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATTTGGCGTCAGTCCTTGc                                               <  1:1664669/71‑1 (MQ=255)
        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                      <  1:1008257/64‑1 (MQ=255)
        ttCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAg                                                      <  1:531635/64‑1 (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)
          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCgg                                             >  1:2815696/1‑71 (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                                             >  1:380270/1‑71 (MQ=255)
          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:3109827/1‑71 (MQ=255)
          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:2598466/1‑71 (MQ=255)
          cAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:1346359/1‑71 (MQ=255)
           aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCgg                                             <  1:5237182/70‑1 (MQ=255)
           aaGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:1717743/1‑60 (MQ=255)
             ggCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGa                                          <  1:4380476/71‑1 (MQ=255)
              gCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAg                                         >  1:548341/1‑71 (MQ=255)
                 gggTTAAGACGTAAGATGCGAAAAGCAGCCATGGATAGAAACTATCTAGCGTCAGTCCTTGCGGGGAGCgg                                      >  1:3351741/1‑71 (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)
                    ttAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCt                                   >  1:5076748/1‑71 (MQ=255)
                    ttAAGACGTAAGATGCGAAAAGAAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCggg                                            <  1:3304238/62‑1 (MQ=255)
                     tAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCtt                                                 <  1:4626194/56‑1 (MQ=255)
                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCtt                                  <  1:2727779/70‑1 (MQ=255)
                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:2894872/1‑49 (MQ=255)
                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:4586445/1‑49 (MQ=255)
                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTc                                                    >  1:3918495/1‑52 (MQ=255)
                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTg                                                >  1:1125942/1‑56 (MQ=255)
                      aaGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTg                                                >  1:852468/1‑56 (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                             <  1:2202383/71‑1 (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                                >  1:4112011/1‑65 (MQ=255)
                             aaGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgta                             >  1:3841719/1‑68 (MQ=255)
                              aGATGCGAAAAGCAGCCATGGACAGAAACTATCTgg                                                            >  1:345136/1‑36 (MQ=255)
                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCa                                                       <  1:1311927/40‑1 (MQ=255)
                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCa                                                       <  1:5604824/40‑1 (MQ=255)
                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:2275215/43‑1 (MQ=255)
                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:1664192/43‑1 (MQ=255)
                               gATGCGAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGTc                                                    <  1:3547129/43‑1 (MQ=255)
                               gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:5440118/1‑40 (MQ=255)
                               gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:4168556/1‑40 (MQ=255)
                               gATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCa                                                       >  1:2913806/1‑40 (MQ=255)
                               gATGCGAAAAGCAGCCATCGACAGAAACTACCTGGCGTc                                                        >  1:1177256/1‑39 (MQ=255)
                                aTGCGAAAAGCAGCCATGGACAGAAACTATCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCg                               >  1:5043737/1‑63 (MQ=255)
                                aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                              <  1:2830334/48‑1 (MQ=255)
                                aTGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACg                                              <  1:2024620/48‑1 (MQ=255)
                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:3422703/1‑37 (MQ=37)
                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:3020164/1‑37 (MQ=37)
                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:2245327/1‑37 (MQ=37)
                                    gAAAAGCAGCCATGGATAGAAACTATCTCGCGTCAGt                                                     >  1:5230840/1‑37 (MQ=37)
                                    gAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCgtagta                          >  1:654207/1‑64 (MQ=255)
                                     aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:4200298/1‑44 (MQ=255)
                                     aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:2010563/1‑44 (MQ=255)
                                     aaaaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:3215063/1‑44 (MQ=255)
                                       aaGCAGCCATGGATAGAAACTATCTCGCGTCAGTCCTTGCggg                                            <  1:4944522/43‑1 (MQ=255)
                                       aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCgg                                             >  1:640366/1‑42 (MQ=255)
                                       aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCgg                                      >  1:2270936/1‑49 (MQ=255)
                                       aaGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCg                                       >  1:1994317/1‑48 (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)
                                                  gACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGa                 <  1:269346/59‑1 (MQ=255)
                                                  gACAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCgtaat                           >  1:4749352/1‑47 (MQ=39)
                                                   aCAGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTCgtaat                           <  1:1560499/48‑3 (MQ=39)
                                                    cAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCttt                                 >  1:4446192/1‑41 (MQ=255)
                                                    cAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGAct               >  1:1316173/1‑59 (MQ=255)
                                                     aGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATTCCCCGCCTCTcccc         >  1:2861394/1‑64 (MQ=255)
                                                     aGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTa  <  1:1925957/71‑1 (MQ=255)
                                                     aGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTc                                >  1:5542994/1‑41 (MQ=255)
                                                     aGAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCTTTc                                >  1:4544381/1‑41 (MQ=255)
                                                      gAAACTACCTGGCGTCAGTCCTTACGGGGAGCGGGCtt                                  <  1:5284256/38‑1 (MQ=255)
                                                           tACCTGACGTCAGTCCTTGCGGGGAGCAGGCTTTCgtaaa                           <  1:1559698/40‑3 (MQ=255)
                                                           tACCTGACGTCAGTCCTTGCGGGGAGCAGGCTTTCgtaaa                           <  1:4986723/40‑3 (MQ=255)
                                                            aCCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTaa                         <  1:5487540/41‑1 (MQ=255)
                                                                ggCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGCCTCTcccc         >  1:3545847/1‑53 (MQ=255)
                                                                ggCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTc      >  1:1927930/1‑56 (MQ=255)
                                                                ggCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACACCGa                 >  1:4164319/1‑45 (MQ=255)
                                                                |                                                           
AGAAGGTATTCAAGGCAGGGTTAAGACGTAAGATGCGAAAAGCAGCCATGGACAGAAACTACCTGGCGTCAGTCCTTGCGGGGAGCGGGCTTTCGTAGTAATACCCCGACTCTCCCCGTCCTTA  >  Exported/218105‑218228

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