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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,208,832 A→G 32.9% H126R (CAC→CGC)  yrdD → predicted DNA topoisomerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,208,8320AG32.9% 84.7 / 70.9 76H126R (CAC→CGC) yrdDpredicted DNA topoisomerase
Reads supporting (aligned to +/- strand):  ref base A (23/28);  new base G (13/12);  total (36/40)
Fisher's exact test for biased strand distribution p-value = 6.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.24e-01

AATTACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCTG  >  W3110S.gb/4208764‑4208900
                                                                    |                                                                    
aaTTACAAGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCAc                                                                     <  1:139509/70‑1 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCActct                                                                  >  1:3654944/1‑70 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCActct                                                                  >  1:3723266/1‑70 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                 >  1:1057638/1‑71 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                 >  1:3650284/1‑71 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                 >  1:3793167/1‑71 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                 >  1:424506/1‑71 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                 >  1:1280768/1‑71 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCtt                                                                 >  1:51116/1‑71 (MQ=255)
   tACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCAGCTCCCGTTATGGCAAAACATTTCActct                                                                  >  1:3664813/1‑70 (MQ=255)
    aCATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTtg                                                                >  1:1805622/1‑71 (MQ=255)
    aCATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCActct                                                                  >  1:3292167/1‑69 (MQ=255)
    aCATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtg                                                                >  1:401861/1‑71 (MQ=255)
    aCATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtg                                                                >  1:711997/1‑71 (MQ=255)
     cATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgt                                                               <  1:300808/71‑1 (MQ=255)
     cATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgt                                                               <  1:4045958/71‑1 (MQ=255)
     cATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgt                                                               <  1:3195843/71‑1 (MQ=255)
      aTGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTtgtg                                                              <  1:2674805/71‑1 (MQ=255)
      aTGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                              <  1:2167162/71‑1 (MQ=255)
         cccccAATGTCGGAC‑‑GCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGc                                                         >  1:485452/1‑71 (MQ=255)
             cAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCt                                                        >  1:220496/1‑70 (MQ=255)
             cAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTa                                                       >  1:1329081/1‑71 (MQ=255)
              aaTGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTAc                                                      <  1:2955126/71‑1 (MQ=255)
                tGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                              <  1:117730/61‑1 (MQ=255)
                 gTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCg                                                   >  1:2371655/1‑71 (MQ=255)
                 gTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCg                                                   >  1:3006040/1‑71 (MQ=255)
                 gTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCg                                                   >  1:3922335/1‑71 (MQ=255)
                  tCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCgg                                                  <  1:2739799/71‑1 (MQ=255)
                  tCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCgg                                                  <  1:3440602/71‑1 (MQ=255)
                  tCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                  <  1:1052516/71‑1 (MQ=255)
                  tCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                  <  1:3007931/71‑1 (MQ=255)
                   cGGACGGGCCATCTGTTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                              <  1:1473070/58‑1 (MQ=255)
                    ggACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTtgtg                                                              <  1:2140191/57‑1 (MQ=255)
                       cGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCt                                                        >  1:32287/1‑60 (MQ=255)
                         ggCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCa                                           <  1:1482858/71‑1 (MQ=255)
                         ggCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCa                                           <  1:4043409/71‑1 (MQ=255)
                          gCCATGTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCa                                           <  1:2827779/70‑1 (MQ=255)
                          gCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCaa                                          >  1:1421609/1‑71 (MQ=255)
                          gCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCaa                                          >  1:3185728/1‑71 (MQ=255)
                          gCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCaa                                          <  1:3768999/71‑1 (MQ=255)
                            cATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTAc                                                      >  1:3011332/1‑57 (MQ=255)
                            cATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAAtt                                        >  1:2864839/1‑71 (MQ=255)
                              tCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCgg                                                  <  1:1807149/59‑1 (MQ=255)
                               cTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                     >  1:144060/1‑71 (MQ=255)
                                tGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                     >  1:3937316/1‑70 (MQ=255)
                                tGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                     >  1:367958/1‑70 (MQ=255)
                                   tCCAGCGCCGCTCCCGTTATTGCAAAAAATTTCActct                                                                  <  1:3021815/38‑1 (MQ=37)
                                   tCCAGCGCCGCTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCAtt                                 <  1:1638478/71‑1 (MQ=255)
                                      aGCGCCGCTCCCGTTATGGCAAAAGATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCAtt                                 <  1:2482914/68‑1 (MQ=255)
                                      aGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAAc                              <  1:2762660/71‑1 (MQ=255)
                                      aGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAAc                              <  1:1638736/71‑1 (MQ=255)
                                         gcagcTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCAt                                  >  1:214328/4‑64 (MQ=255)
                                          ccgcTCCCGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCa                          <  1:1611384/71‑1 (MQ=255)
                                          ccgcTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTc                           >  1:999246/1‑70 (MQ=255)
                                                ccGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGc                                     <  1:2019039/54‑1 (MQ=255)
                                                ccGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAAccc                     <  1:1252431/70‑1 (MQ=255)
                                                 cGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCAt                   <  1:35853/71‑1 (MQ=255)
                                                 cGTTATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCAt                   <  1:2837309/71‑1 (MQ=255)
                                                   ttATGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTc                                            <  1:2242457/44‑1 (MQ=255)
                                                   ttATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCa                                           <  1:1581975/45‑1 (MQ=255)
                                                   ttATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAAcc                      <  1:2195180/66‑1 (MQ=255)
                                                    tATGGCAAAACATTTCACTCTTGTGATCGCTAccc                                                    >  1:400838/1‑35 (MQ=255)
                                                     aTGGCAAAACATTTCGCTCTTGTGATCGCTACCCGGAGTGTCa                                           <  1:2544712/43‑1 (MQ=255)
                                                     aTGGCAAAACATTTCACTCTTGTGATCGCTACCCGGa                                                 >  1:595039/1‑37 (MQ=255)
                                                     aTGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAAtt                                        >  1:752395/1‑46 (MQ=255)
                                                     aTGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCt               >  1:66178/1‑71 (MQ=255)
                                                      tGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATa                  <  1:1681502/67‑1 (MQ=255)
                                                      tGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATa                  <  1:3315478/67‑1 (MQ=255)
                                                        gCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGc                >  1:634883/1‑67 (MQ=255)
                                                         cAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGgag           <  1:3101420/71‑1 (MQ=255)
                                                          aaaaCATTTCACTCTTGTGATCGCTACCGGGAGTGTCa                                           <  1:438063/38‑1 (MQ=255)
                                                          aaaaCATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCaaa                        >  1:688551/1‑57 (MQ=255)
                                                                tttCGCTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGccc    >  1:1294031/1‑71 (MQ=255)
                                                                tttCACTCTTGTGATCGCTACCCGGAGTGTCAAttt                                       <  1:2571188/36‑1 (MQ=255)
                                                                   cACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCTg  <  1:1154817/70‑1 (MQ=255)
                                                                   cACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCTg  <  1:3823411/70‑1 (MQ=255)
                                                                    |                                                                    
AATTACATGCCCCCAATGTCGGACGGGCCATCTGGTCCAGCGCCGCTCCCGTTATGGCAAAACATTTCACTCTTGTGATCGCTACCCGGAGTGTCAATTTGCCATTAACTTCAAACCCATAGCTGGAGAATGCCCTG  >  W3110S.gb/4208764‑4208900

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