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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,295,635 T→C 41.0% Y178H (TAC→CAC)  tdk → thymidine kinase/deoxyuridine kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,295,6350TC41.0% 44.7 / 104.9 83Y178H (TAC→CAC) tdkthymidine kinase/deoxyuridine kinase
Reads supporting (aligned to +/- strand):  ref base T (22/27);  new base C (19/15);  total (41/42)
Fisher's exact test for biased strand distribution p-value = 3.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.96e-01

TCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGGA  >  W3110S.gb/1295571‑1295702
                                                                |                                                                   
tCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGttt                                                               >  1:3515471/1‑71 (MQ=255)
tCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGtt                                                                >  1:1873194/1‑70 (MQ=255)
    gATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTg                                                            >  1:4760935/1‑70 (MQ=255)
    gATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTg                                                            >  1:139178/1‑70 (MQ=255)
    gATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTg                                                            >  1:2723190/1‑70 (MQ=255)
      tCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTAt                                                         >  1:865700/1‑71 (MQ=255)
       cAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTAt                                                         >  1:3048578/1‑70 (MQ=255)
       cAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATg                                                        >  1:2911189/1‑71 (MQ=255)
            aggcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTa                                                   <  1:917032/71‑1 (MQ=255)
              gcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGAt                                                                     <  1:4257927/51‑1 (MQ=255)
              gcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGAt                                                                     <  1:561603/51‑1 (MQ=255)
              gcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTa                                                          >  1:3439048/1‑62 (MQ=255)
              gcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTaaa                                                 <  1:1777369/71‑1 (MQ=255)
                agACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAaca                                               >  1:130738/1‑71 (MQ=255)
                agACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAaca                                               >  1:294374/1‑71 (MQ=255)
                agACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAaca                                               >  1:3886925/1‑71 (MQ=255)
                   ccTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACta                                            <  1:3043426/71‑1 (MQ=255)
                   ccTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACta                                            <  1:1709925/71‑1 (MQ=255)
                    cTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACta                                            >  1:4758445/1‑70 (MQ=255)
                      tataACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACtata                                          >  1:2752786/1‑70 (MQ=255)
                       ataACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACtata                                          >  1:1731171/1‑69 (MQ=255)
                       ataACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAaca                                               >  1:2039850/1‑64 (MQ=255)
                       ataACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAaca                                               >  1:4192684/1‑64 (MQ=255)
                        taACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATaaa                                        <  1:5022200/70‑1 (MQ=255)
                        taACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACtata                                          >  1:907620/1‑68 (MQ=255)
                         aaCGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACg                                                                  >  1:372659/1‑43 (MQ=255)
                         aaCGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACg                                                                  >  1:2216427/1‑43 (MQ=255)
                         aaCGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACg                                                                  >  1:3976188/1‑43 (MQ=255)
                          aCGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAagag                                     >  1:4652399/1‑71 (MQ=255)
                           cGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAgg                                    <  1:303841/71‑1 (MQ=255)
                           cGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAgg                                    <  1:924039/71‑1 (MQ=255)
                            gAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGc                                   >  1:749853/1‑71 (MQ=255)
                               ggTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGt                                 >  1:3783585/1‑70 (MQ=255)
                                 tGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAGGAGGCGTTAc                              <  1:3700532/71‑1 (MQ=255)
                                 tGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTa                                                          >  1:3702781/1‑43 (MQ=255)
                                 tGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTa                                                          >  1:1331578/1‑43 (MQ=255)
                                  gAGCAGGTGGTAATTGGTGGTAATGAACGATACGt                                                                 <  1:4111532/35‑1 (MQ=255)
                                   aGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACaa                            <  1:3366841/71‑1 (MQ=255)
                                   aGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTa                                                          >  1:5107969/1‑41 (MQ=255)
                                   aGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTa                                                          >  1:3895417/1‑41 (MQ=255)
                                    gCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAg                           >  1:2693266/1‑71 (MQ=255)
                                     cAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGt                          >  1:5108619/1‑71 (MQ=255)
                                      aGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTc                         <  1:1288901/71‑1 (MQ=255)
                                        gtggtAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTa                                                   <  1:336985/43‑1 (MQ=255)
                                        gtggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaa                                         <  1:4183598/53‑1 (MQ=255)
                                        gtggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaa                                         <  1:1060694/53‑1 (MQ=255)
                                         tggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTa                                                   <  1:3551818/42‑1 (MQ=255)
                                         tggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaa                                         <  1:628713/52‑1 (MQ=255)
                                         tggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGAc                      <  1:2863029/71‑1 (MQ=255)
                                          ggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACt                     >  1:3978401/1‑71 (MQ=255)
                                           gtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTc                    <  1:4837970/71‑1 (MQ=255)
                                              aTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATaaa                                        <  1:2375748/48‑1 (MQ=255)
                                              aTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATaaa                                        <  1:2270676/48‑1 (MQ=255)
                                               ttGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGt                          >  1:2932546/1‑61 (MQ=255)
                                               ttGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTa                <  1:4833116/71‑1 (MQ=255)
                                               ttGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTa                <  1:2190181/71‑1 (MQ=255)
                                               ttGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaaa                                        <  1:249402/47‑1 (MQ=255)
                                               ttGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaaa                                        <  1:75332/47‑1 (MQ=255)
                                               ttGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaaa                                        <  1:139822/47‑1 (MQ=255)
                                                tggtggTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGt                                 <  1:946898/53‑1 (MQ=255)
                                                tggtggTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGt                                 <  1:2790624/53‑1 (MQ=255)
                                                tggtggTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCAtt                 <  1:144160/69‑1 (MQ=255)
                                                     gtAATGAACGATACGTTTCTGTATGCCGTAAACACta                                            <  1:4670979/37‑1 (MQ=255)
                                                     gtAATGAACGATACGTTTCTGTATGCCGTAAACACta                                            <  1:4676788/37‑1 (MQ=255)
                                                      tAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACt                     <  1:926915/59‑1 (MQ=255)
                                                      tAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTa                <  1:3860306/64‑1 (MQ=255)
                                                      tAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTa                <  1:2183797/64‑1 (MQ=255)
                                                       aaTGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCAtt                 <  1:4288723/62‑1 (MQ=255)
                                                        aTGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACa                             <  1:747877/49‑1 (MQ=255)
                                                        aTGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACa                             <  1:3090195/49‑1 (MQ=255)
                                                         tGAACGATACGTTTCTGTATGCCGTAAACACtata                                          <  1:1089016/35‑1 (MQ=255)
                                                         tGAACGATACGTTTCTGTATGCCGTAAACACtata                                          <  1:2347600/35‑1 (MQ=255)
                                                          gAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTaa               >  1:3238862/1‑61 (MQ=255)
                                                          gAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTAtt       >  1:1329511/1‑69 (MQ=255)
                                                          gAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTAtt       >  1:4362170/1‑69 (MQ=255)
                                                          gAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACCAGTCGACTCATTAACGGCTAtt       >  1:4700555/1‑69 (MQ=255)
                                                           aaCGATACGTTTCTGTATGCCGTAAACACTATaaa                                        >  1:3270130/1‑35 (MQ=255)
                                                           aaCGATACGTTTCTGTATGCCGTAAACACTATaaa                                        >  1:5014607/1‑35 (MQ=255)
                                                           aaCGATACGTTTCTGTATGCCGTAAACACTATaaa                                        >  1:1140961/1‑35 (MQ=255)
                                                           aaCGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAg    >  1:294686/1‑71 (MQ=255)
                                                            aCGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTa                >  1:722399/1‑58 (MQ=255)
                                                             cGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGGa  <  1:3401758/71‑1 (MQ=255)
                                                               aTACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGt                                 <  1:4298015/38‑1 (MQ=255)
                                                               aTACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGGa  <  1:4644976/69‑1 (MQ=255)
                                                               aTACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGGa  <  1:3834401/69‑1 (MQ=255)
                                                                |                                                                   
TCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGGA  >  W3110S.gb/1295571‑1295702

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