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 F17 I0 R1 87 56.5 4283937 98.6% 4223961 62.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,295,635 T→C 7.9% 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.gb1,295,6350TC 7.9% 241.5 / 11.8 89Y178H (TAC→CAC) tdkthymidine kinase/deoxyuridine kinase
Reads supporting (aligned to +/- strand):  ref base T (48/34);  new base C (4/3);  total (52/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

CTGCGTCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGG  >  W3110S.gb/1295566‑1295701
                                                                     |                                                                  
ctgcGTCTAGATCAATCAGGCAGACCTTATAACGAAGGAGAGCAGGTGGTAATTGGTGGTAATGAACGATa                                                                   >  1:2897547/1‑71 (MQ=255)
 tgcGTCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATAc                                                                  >  1:2753776/1‑71 (MQ=255)
  gcGTCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACg                                                                 >  1:1954276/1‑71 (MQ=255)
  gcGTCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACg                                                                 >  1:1572960/1‑71 (MQ=255)
   cGTCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATAc                                                                  <  1:2671014/69‑1 (MQ=255)
       ttGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCt                                                            >  1:2035926/1‑71 (MQ=255)
       ttGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCt                                                            >  1:3237695/1‑71 (MQ=255)
       ttGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCt                                                            >  1:3714864/1‑71 (MQ=255)
        tGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTg                                                           >  1:538694/1‑71 (MQ=255)
         gATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTg                                                           <  1:693827/70‑1 (MQ=255)
          aTCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTg                                                           >  1:1202581/1‑69 (MQ=255)
           tCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTAt                                                        >  1:4036877/1‑71 (MQ=255)
              aGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATa                                                                   >  1:2099021/1‑57 (MQ=255)
               gcaggcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCg                                                    >  1:3711191/1‑71 (MQ=255)
                 aggcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTg                                                           <  1:1613613/62‑1 (MQ=255)
                 aggcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTa                                                  <  1:3532707/71‑1 (MQ=255)
                 aggcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTa                                                  <  1:2025799/71‑1 (MQ=255)
                   gcggACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTaaa                                                <  1:2709851/68‑1 (MQ=255)
                   gcagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTaaa                                                <  1:1092242/71‑1 (MQ=255)
                    cagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTaaa                                                >  1:3512675/1‑70 (MQ=255)
                    cagACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTaaa                                                >  1:2256417/1‑70 (MQ=255)
                     agACATTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAaca                                              >  1:2418793/1‑71 (MQ=255)
                      gACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAacac                                             <  1:756710/71‑1 (MQ=255)
                      gACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAacac                                             <  1:2788275/71‑1 (MQ=255)
                       aCCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAacac                                             >  1:1199892/1‑70 (MQ=255)
                       aCCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACt                                            <  1:1201892/71‑1 (MQ=255)
                        ccTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACta                                           >  1:654061/1‑71 (MQ=255)
                         cTTATAACGAAGGTGAGCAGTTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACta                                           >  1:3830334/1‑70 (MQ=255)
                         cTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACta                                           >  1:1810376/1‑70 (MQ=255)
                         cTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACta                                           >  1:2737889/1‑70 (MQ=255)
                          ttATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTa                                                  <  1:2126081/62‑1 (MQ=255)
                          ttATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACtat                                          <  1:2396578/70‑1 (MQ=255)
                            ataACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACtata                                         <  1:2276242/69‑1 (MQ=255)
                            ataACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACtat                                          >  1:691871/1‑68 (MQ=255)
                             taACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATaaa                                       <  1:2933160/70‑1 (MQ=255)
                             taACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATaaa                                       <  1:3047305/70‑1 (MQ=255)
                             taACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAag                                      <  1:52915/71‑1 (MQ=255)
                             taACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAag                                      <  1:3637389/71‑1 (MQ=255)
                              aaCGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTa                                                  <  1:1685846/58‑1 (MQ=255)
                                 gAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGc                                  >  1:3520258/1‑71 (MQ=255)
                                 gAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTg                                                           <  1:1874799/46‑1 (MQ=255)
                                  aaGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCg                                 <  1:607010/71‑1 (MQ=255)
                                   aGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGt                                >  1:2947979/1‑71 (MQ=255)
                                   aGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGt                                <  1:3704400/71‑1 (MQ=255)
                                   aGGTGAGCAGGTGGTAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATaaa                                       >  1:3366198/1‑64 (MQ=255)
                                    ggTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTc                                                             >  1:1628784/1‑41 (MQ=255)
                                    ggTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTaaa                                                <  1:749365/54‑1 (MQ=255)
                                      tGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTAc                             <  1:1423441/71‑1 (MQ=255)
                                       gAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAacac                                             >  1:687204/1‑54 (MQ=255)
                                       gAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACtat                                          <  1:3373869/57‑1 (MQ=255)
                                       gAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTAc                             >  1:1962481/1‑70 (MQ=255)
                                       gAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTAc                             >  1:2572646/1‑70 (MQ=255)
                                        aGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTAc                             >  1:851122/1‑69 (MQ=255)
                                        aGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTAc                             >  1:1041870/1‑69 (MQ=255)
                                           aGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTc                        <  1:2756654/71‑1 (MQ=255)
                                           aGGTGGTAATTGGTGGTAATGAACGATACGTTTCTCTATGCCGTAAACACTATAAAGAGGCGTTACAAGTc                        <  1:1411925/71‑1 (MQ=255)
                                             gtggtAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTc                        <  1:1109469/69‑1 (MQ=255)
                                              tggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGAc                     <  1:998887/71‑1 (MQ=255)
                                              tggtAATTGGTGGTAATGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGAc                     <  1:1064249/71‑1 (MQ=255)
                                               ggtAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCg                                 >  1:719293/1‑58 (MQ=255)
                                                gtAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGAc                     <  1:133196/69‑1 (MQ=255)
                                                 tAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACt                    <  1:2968613/69‑1 (MQ=255)
                                                  aaTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTAc                             >  1:4170261/1‑59 (MQ=255)
                                                  aaTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCaa                 >  1:3321541/1‑70 (MQ=255)
                                                  aaTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCAt                 >  1:2863710/1‑71 (MQ=255)
                                                   aTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTc                        <  1:1376939/63‑1 (MQ=255)
                                                   aTTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGAc                     <  1:1002389/66‑1 (MQ=255)
                                                   aTTGGTGGTAATGAACCATACGTTTCTGTATGCCGTaaa                                                >  1:3058987/1‑39 (MQ=255)
                                                    ttGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACt                                            <  1:2558862/42‑1 (MQ=255)
                                                    ttGGTGGTAATGAACGATACGTTTCTGTATGCCGCAAACACTATAAAGAGGCGTTACAAGTCGACTCATTa               <  1:2711565/71‑1 (MQ=255)
                                                      ggtggtAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGAc                     >  1:1518931/1‑63 (MQ=255)
                                                      ggtggtAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAAc             >  1:4111272/1‑71 (MQ=255)
                                                      ggtggtAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAAc             >  1:4269258/1‑71 (MQ=255)
                                                         ggtAATGAACGATACGTTTCTGTATGCCGTAAacac                                             >  1:2414326/1‑36 (MQ=255)
                                                         ggtAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAAcata          >  1:2419426/1‑68 (MQ=255)
                                                           tAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCa                  >  1:4162102/1‑61 (MQ=255)
                                                            aaTGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTAt       >  1:1564547/1‑71 (MQ=255)
                                                            aaTGAACGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTAt       >  1:1054015/1‑71 (MQ=255)
                                                             aTGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACaa                           >  1:1150063/1‑50 (MQ=255)
                                                             aTGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAg                          >  1:3547508/1‑51 (MQ=255)
                                                             aTGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTAtt      <  1:1198866/71‑1 (MQ=255)
                                                              tGAACGATACGTTTCTGTATGCCGTAAACACTATaaa                                       <  1:2542211/37‑1 (MQ=255)
                                                              tGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTAtt      >  1:877604/1‑70 (MQ=255)
                                                                aaCGATACGTTTCTGTATGCCGTAAACACTATAAaga                                     >  1:3532308/1‑37 (MQ=255)
                                                                aaCGATACGTTTCTGTATGCCGTAAACACTATAAaga                                     >  1:1345901/1‑37 (MQ=255)
                                                                aaCGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAg   >  1:2822502/1‑71 (MQ=255)
                                                                aaCGACACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAg   >  1:3624403/1‑71 (MQ=255)
                                                                 aCGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCa    >  1:3131226/1‑69 (MQ=255)
                                                                  cGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAgg  >  1:3684304/1‑70 (MQ=255)
                                                                     |                                                                  
CTGCGTCTTGATCAAGCAGGCAGACCTTATAACGAAGGTGAGCAGGTGGTAATTGGTGGTAATGAACGATACGTTTCTGTATGCCGTAAACACTATAAAGAGGCGTTACAAGTCGACTCATTAACGGCTATTCAGG  >  W3110S.gb/1295566‑1295701

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