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
A1 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,960,805 T→C 27.3% K94E (AAA→GAA)  recC ← exonuclease V (RecBCD complex), gamma chain

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,960,8050TC27.3% 84.8 / 37.9 55K94E (AAA→GAA) recCexonuclease V (RecBCD complex), gamma chain
Reads supporting (aligned to +/- strand):  ref base T (18/22);  new base C (8/7);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 7.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGATAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCGGACGAACATATC  >  W3110S.gb/2960741‑2960874
                                                                |                                                                     
agATAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCt                                                                 >  1:1102879/1‑71 (MQ=255)
agATAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCt                                                                 <  1:2907066/71‑1 (MQ=255)
agATAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCt                                                                 <  1:216056/71‑1 (MQ=255)
  aTAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCa                                                               >  1:2291301/1‑71 (MQ=255)
   tAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCAt                                                              >  1:1621556/1‑71 (MQ=255)
     aTGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATg                                                             <  1:983534/70‑1 (MQ=255)
     aTGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATg                                                             <  1:4222699/70‑1 (MQ=255)
     aTGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATg                                                             <  1:3731430/70‑1 (MQ=255)
     aTGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATg                                                             <  1:3044466/70‑1 (MQ=255)
     aTGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGc                                                            >  1:848954/1‑71 (MQ=255)
     aTGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGc                                                            >  1:1123110/1‑71 (MQ=255)
      tGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGct                                                           >  1:2504413/1‑71 (MQ=255)
         cGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCtg                                                        <  1:497561/71‑1 (MQ=255)
         cGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCtg                                                        <  1:2350377/71‑1 (MQ=255)
            aaCAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCt                                                                 <  1:2838695/59‑1 (MQ=255)
             aCAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCtgtttg                                                    <  1:283698/71‑1 (MQ=255)
             aCAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCtgtt                                                      <  1:3230851/69‑1 (MQ=255)
                gggTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTa                                                 <  1:3527651/71‑1 (MQ=255)
                 ggTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGct                                                           <  1:2000782/60‑1 (MQ=255)
                   tAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAg                                              >  1:1472283/1‑71 (MQ=255)
                   tAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAg                                              <  1:2071806/71‑1 (MQ=255)
                     aaGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGgc                                            >  1:1422639/1‑71 (MQ=255)
                       gTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTcc                                                                     <  1:647683/44‑1 (MQ=255)
                        tCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCtgtttgtt                                                  <  1:3720998/62‑1 (MQ=255)
                         cTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAg                                                                   >  1:3931594/1‑44 (MQ=255)
                          ttCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGctct                                       >  1:3202061/1‑71 (MQ=255)
                          ttCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGct                                         >  1:2535083/1‑69 (MQ=255)
                          ttCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTAAAGGCGctct                                       >  1:182061/1‑71 (MQ=255)
                             gcgcTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCtt                                    <  1:2327206/71‑1 (MQ=255)
                                cTCCAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTgg                                 >  1:253633/1‑71 (MQ=255)
                                   cAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTgggg                               <  1:3731541/70‑1 (MQ=255)
                                   cAGCAATTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGa                              >  1:1362950/1‑71 (MQ=255)
                                    aGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCtt                                    <  1:2613722/64‑1 (MQ=255)
                                     gCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTc                                                                <  1:2630177/35‑1 (MQ=255)
                                     gCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCa                                                               >  1:1639464/1‑36 (MQ=255)
                                     gCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTaa                                                >  1:3672798/1‑51 (MQ=255)
                                       aaTTGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTc                          >  1:1097933/1‑71 (MQ=255)
                                         ttGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTa                                                 <  1:4177685/46‑1 (MQ=255)
                                         ttGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCtt                                    <  1:2535469/59‑1 (MQ=255)
                                         ttGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTcc                         <  1:2032855/70‑1 (MQ=255)
                                         ttGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTcc                         <  1:4093739/70‑1 (MQ=255)
                                         ttGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCg                        <  1:4322629/71‑1 (MQ=255)
                                          tGCGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGAt                             >  1:2781745/1‑65 (MQ=255)
                                           gCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCgg                       >  1:2342219/1‑70 (MQ=255)
                                           gCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCgg                       >  1:1341533/1‑70 (MQ=255)
                                           gCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCgg                       >  1:2678727/1‑70 (MQ=255)
                                           gCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTATGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCgg                       >  1:1358633/1‑70 (MQ=255)
                                            cGGCAGCAGAGTCATCAGTTCCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGt                      <  1:3848397/70‑1 (MQ=255)
                                             ggCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTaa                    <  1:4268373/71‑1 (MQ=255)
                                                   agagTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCg              <  1:4413587/71‑1 (MQ=255)
                                                   agagTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCg              >  1:1635231/1‑71 (MQ=255)
                                                       tcatcaGTTTCCAGCTCATGCTCTGTTTGTTAAAgg                                             >  1:2382233/1‑36 (MQ=255)
                                                         atcaGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCGGACGaa        >  1:3277495/1‑71 (MQ=255)
                                                         atcaGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCGGACGaa        <  1:2059709/71‑1 (MQ=255)
                                                         atcaGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCGGACGaa        >  1:1560633/1‑71 (MQ=255)
                                                              tttCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCg              <  1:2114868/60‑1 (MQ=255)
                                                               ttCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCGGACGAACATATc  >  1:130544/1‑71 (MQ=255)
                                                                |                                                                     
AGATAATGCCGCAACAGGGTAAAGTCTTCGCGCTCCAGCAATTGCGGCAGCAGAGTCATCAGTTTCCAGCTCATGCTCTGTTTGTTAAAGGCGCTCTCTTTGGGGATTTCCGGTAACACCCGGACGAACATATC  >  W3110S.gb/2960741‑2960874

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