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 4,208,832 A→G 26.7% H126R (CAC→CGC)  yrdD → predicted DNA topoisomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,208,8320AG26.7% 92.9 / 40.6 60H126R (CAC→CGC) yrdDpredicted DNA topoisomerase
Reads supporting (aligned to +/- strand):  ref base A (19/25);  new base G (6/10);  total (25/35)
Fisher's exact test for biased strand distribution p-value = 7.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.39e-01

GCAATTACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCT  >  W3110S.gb/4208762‑4208899
                                                                      |                                                                   
gCAATTACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCa                                                                     >  1:861525/1‑71 (MQ=255)
    ttACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCActct                                                                 >  1:4531173/1‑71 (MQ=255)
     tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                >  1:119675/1‑71 (MQ=255)
      aCATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtg                                                               >  1:99479/1‑71 (MQ=255)
        aTGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                             <  1:365968/71‑1 (MQ=255)
        aTGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                             <  1:2859070/71‑1 (MQ=255)
         tGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                             <  1:185138/70‑1 (MQ=255)
           cccccAATGTCGGACGGGCCATCTGGTCCAGCGCCGGTCCCGTTATGGCAAAACATTTCGCTCTTGTGa                                                            <  1:4366635/69‑1 (MQ=255)
              ccAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCt                                                       <  1:4474369/71‑1 (MQ=255)
               cAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCg                                                         >  1:4573490/1‑68 (MQ=255)
               cAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTa                                                      <  1:3612325/71‑1 (MQ=255)
                 aTGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCtt                                                                <  1:3999077/59‑1 (MQ=255)
                 aTGTCGGACGGGCCATCTGGTCCAGCGCAGCTCCCGTTATGGGAAAACATTTCa                                                                     >  1:2353509/1‑54 (MQ=255)
                    tCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTAcc                                                    >  1:4623708/1‑68 (MQ=255)
                            gCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCaa                                         <  1:3780247/71‑1 (MQ=255)
                            gCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCaa                                         <  1:512465/71‑1 (MQ=255)
                             ccATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAAt                                        >  1:3110082/1‑71 (MQ=255)
                             ccATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                 <  1:4038234/62‑1 (MQ=255)
                             ccATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                 <  1:3226550/62‑1 (MQ=255)
                               aTCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAg                                               >  1:3424425/1‑62 (MQ=255)
                                tCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTa                                                      <  1:707906/54‑1 (MQ=255)
                                 cTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                    >  1:285331/1‑71 (MQ=255)
                                 cTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                    >  1:4341309/1‑71 (MQ=255)
                                  tGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCa                                                                     >  1:1581754/1‑37 (MQ=255)
                                  tGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                    >  1:2017769/1‑70 (MQ=255)
                                  tGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGAt                                                           >  1:2546343/1‑47 (MQ=255)
                                  tGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                    >  1:2304039/1‑70 (MQ=255)
                                    gTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                    <  1:701663/68‑1 (MQ=255)
                                     tCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTtg                                                               <  1:409608/40‑1 (MQ=255)
                                     tCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCAtt                                <  1:294726/71‑1 (MQ=255)
                                     tCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCAtt                                <  1:3868828/71‑1 (MQ=255)
                                       cAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTaa                              >  1:2134684/1‑71 (MQ=255)
                                        aGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAAc                             <  1:54247/71‑1 (MQ=255)
                                         gcgcCGCTCCCGTTATGGCAAAACATTTCGCTCTtgtg                                                             <  1:2025157/38‑1 (MQ=255)
                                          cgccgcTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCa                                          <  1:1036516/56‑1 (MQ=255)
                                           gccgcTCCCGTTATGGCAAAACATTTCACTCTtgt                                                              >  1:4508182/1‑35 (MQ=255)
                                           gccgcTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                 <  1:3877803/48‑1 (MQ=255)
                                             cgcTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTCCCCGGAGTGTCAATTTGCCATTAACTTCa                         >  1:3315109/1‑70 (MQ=255)
                                              gcTCCCGTTATGGCAAAACATTTCACTCTTGTGATc                                                          >  1:3595690/1‑36 (MQ=255)
                                               cTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                 <  1:550146/44‑1 (MQ=255)
                                                 cccGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAAtt                                       >  1:3743082/1‑52 (MQ=255)
                                                  ccGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCaa                                         <  1:647907/49‑1 (MQ=255)
                                                  ccGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAAccc                    <  1:645850/70‑1 (MQ=255)
                                                  ccGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAAccc                    <  1:2513653/70‑1 (MQ=255)
                                                    gTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCa                                  >  1:2890494/1‑54 (MQ=255)
                                                     ttATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAAt                                        <  1:2770659/47‑1 (MQ=255)
                                                     ttATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCa                         <  1:1117655/62‑1 (MQ=255)
                                                     ttATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCa                         <  1:285490/62‑1 (MQ=255)
                                                      tATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGc               >  1:3993211/1‑71 (MQ=255)
                                                      tATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGc               >  1:982961/1‑71 (MQ=255)
                                                          gCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGga           <  1:652945/71‑1 (MQ=255)
                                                          gCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGga           <  1:1240990/71‑1 (MQ=255)
                                                           cAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGgag          <  1:60206/71‑1 (MQ=255)
                                                            aaaaCATTTCACTCTTGTGATCGCTACCCGGAGTGTCaa                                         >  1:785972/1‑39 (MQ=255)
                                                             aaaCATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGaa        <  1:844622/71‑1 (MQ=255)
                                                              aaCATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGgag          <  1:1138807/68‑1 (MQ=255)
                                                              aaCATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAAt       <  1:3146497/71‑1 (MQ=255)
                                                               aCATTTCACTCTTGTGATCGCTACCCGGAGTGTCAAtt                                       >  1:647389/1‑38 (MQ=255)
                                                                cATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGc     >  1:2422615/1‑71 (MQ=255)
                                                                 aTTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCa                                  >  1:3997331/1‑41 (MQ=255)
                                                                 aTTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGcc    <  1:4472834/71‑1 (MQ=255)
                                                                  tttCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGccc   <  1:2918562/71‑1 (MQ=255)
                                                                    tCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCt  >  1:7925/1‑70 (MQ=255)
                                                                      |                                                                   
GCAATTACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCT  >  W3110S.gb/4208762‑4208899

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