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 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,253,271 C→T 11.9% V99V (GTC→GTT)  yhaK → predicted pirin‑related protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,253,2710CT11.9% 196.7 / 13.6 67V99V (GTC→GTT) yhaKpredicted pirin‑related protein
Reads supporting (aligned to +/- strand):  ref base C (31/28);  new base T (3/5);  total (34/33)
Fisher's exact test for biased strand distribution p-value = 4.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGATAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCTG  >  W3110S.gb/3253201‑3253339
                                                                      |                                                                    
gcgATAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTc                                                                      <  1:1717118/71‑1 (MQ=255)
   aTAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGc                                                                   <  1:1288676/71‑1 (MQ=255)
    tAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCT‑CTCTCTACCCAGCCGGGTGTCAGCta                                                                 <  1:943390/71‑1 (MQ=255)
     aGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCta                                                                 >  1:2535107/1‑71 (MQ=255)
              aaTCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAaca                                                        <  1:2734301/71‑1 (MQ=255)
                tCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAacac                                                       >  1:3365075/1‑70 (MQ=255)
                tCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCGCTCTACCCAGCCGGGTGTCAGCtat                                                                <  1:3114425/61‑1 (MQ=255)
                 cATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCCGCCGGGTGTCAGCTATAGCGAaca                                                        >  1:2379753/1‑68 (MQ=255)
                 cATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACaa                                                     >  1:4581859/1‑71 (MQ=255)
                    gTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGaa                                                          >  1:3407982/1‑63 (MQ=255)
                     ttCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCta                                                                 <  1:582021/55‑1 (MQ=255)
                     ttCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAAt                                                    <  1:58434/68‑1 (MQ=255)
                         ggCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCa                                             <  1:3727493/71‑1 (MQ=255)
                            cAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCa                                             >  1:1437506/1‑68 (MQ=255)
                            cAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGa                                                           <  1:491405/54‑1 (MQ=255)
                            cAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAAtc                                                   >  1:1424981/1‑62 (MQ=255)
                            cAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCa                                             >  1:1459730/1‑68 (MQ=255)
                               cgcCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGAc                                        >  1:1059104/1‑70 (MQ=255)
                                 ccGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAg                                               <  1:2248705/61‑1 (MQ=255)
                                 ccGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCaaa                                           >  1:940250/1‑65 (MQ=255)
                                 ccGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACaa                                      >  1:1075355/1‑70 (MQ=255)
                                   ggAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAAtc                                                   <  1:2702932/55‑1 (MQ=255)
                                    gagaGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCg                                  >  1:189723/1‑71 (MQ=255)
                                     agagGCGTTGCTGCTCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGt                                 <  1:2957907/71‑1 (MQ=255)
                                     agagGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGt                                 <  1:1723871/71‑1 (MQ=255)
                                      gagGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAAc                                    >  1:3939593/1‑67 (MQ=255)
                                       agGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGtt                                >  1:478677/1‑70 (MQ=255)
                                        ggCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTaa                              >  1:4330547/1‑71 (MQ=255)
                                         gCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAc                             <  1:2962463/71‑1 (MQ=255)
                                         gCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAc                             <  1:1718668/71‑1 (MQ=255)
                                           gTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCg                                  <  1:1629326/64‑1 (MQ=255)
                                           gTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgc                           >  1:3732434/1‑71 (MQ=255)
                                            ttGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAg                                          <  1:3106138/55‑1 (MQ=255)
                                            ttGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:3606393/71‑1 (MQ=255)
                                             tgctgcTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          >  1:1498027/1‑70 (MQ=255)
                                             tgctgcTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          >  1:2122902/1‑70 (MQ=255)
                                              gctgctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGaa                        >  1:387458/1‑71 (MQ=255)
                                                tgctCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCa                                             <  1:912946/48‑1 (MQ=255)
                                                tgctCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCa                                             <  1:919942/48‑1 (MQ=255)
                                                tgctCTCTACCCAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATg                      >  1:1001638/1‑71 (MQ=255)
                                                tgctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAcgcg                          <  1:2506448/67‑1 (MQ=255)
                                                tgctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGa                         <  1:2485344/68‑1 (MQ=255)
                                                 gctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCg                                  <  1:534522/58‑1 (MQ=255)
                                                 gctCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATg                      >  1:3847560/1‑70 (MQ=255)
                                                  ctctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGtt                                <  1:1333984/59‑1 (MQ=255)
                                                  ctctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGc                     <  1:4196354/70‑1 (MQ=255)
                                                   tctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCa                    >  1:1009158/1‑70 (MQ=255)
                                                    ctctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGc                  >  1:2224858/1‑71 (MQ=255)
                                                     tctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGAc                                        >  1:4559483/1‑48 (MQ=255)
                                                     tctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGtt                                <  1:2419866/56‑1 (MQ=255)
                                                     tctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAAc                             <  1:3951560/59‑1 (MQ=255)
                                                     tctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCt                 >  1:4599051/1‑71 (MQ=255)
                                                     tctACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCt                 >  1:3844977/1‑71 (MQ=255)
                                                       tACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGtt                                <  1:3092556/54‑1 (MQ=255)
                                                        aCCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCttt               <  1:2197872/70‑1 (MQ=255)
                                                         cccAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTgg             >  1:3283331/1‑71 (MQ=255)
                                                         cccAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTgg             >  1:2978336/1‑71 (MQ=255)
                                                         cccAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTg              <  1:4612296/70‑1 (MQ=255)
                                                          ccAGCCGGGTGTTAGCTATAGCGAACACAATCTCAGCAAAGACaa                                      >  1:4505755/1‑45 (MQ=255)
                                                           cAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCt                 <  1:4557488/65‑1 (MQ=255)
                                                            aGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTg          >  1:993079/1‑71 (MQ=255)
                                                            aGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTg          >  1:989643/1‑71 (MQ=255)
                                                            aGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTg          <  1:4543018/71‑1 (MQ=255)
                                                                gggTGTTAGCTATAGCGAACACAATCTCAGCAAAGACaa                                      <  1:4542399/39‑1 (MQ=255)
                                                                 ggTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGc     >  1:793377/1‑71 (MQ=255)
                                                                 ggTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGc     <  1:3640583/71‑1 (MQ=255)
                                                                   tgtCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAAt                       >  1:2722603/1‑51 (MQ=255)
                                                                    gtCAGCGATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCTg  >  1:592733/1‑71 (MQ=255)
                                                                      |                                                                    
GCGATAGCGAAGGCAATCATGTTCAGGCCAGCGCCGGAGAGGCGTTGCTGCTCTCTACCCAGCCGGGTGTCAGCTATAGCGAACACAATCTCAGCAAAGACAAACCGTTAACGCGAATGCAGCTTTGGCTGGACGCCTG  >  W3110S.gb/3253201‑3253339

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A