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 3,306,434 G→A 13.5% L428L (CTG→TTG)  deaD ← ATP‑dependent RNA helicase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,306,4340GA13.5% 163.7 / 15.0 59L428L (CTG→TTG) deaDATP‑dependent RNA helicase
Reads supporting (aligned to +/- strand):  ref base G (28/23);  new base A (4/4);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGTTTCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTCAGCAGTGCG  >  W3110S.gb/3306365‑3306504
                                                                     |                                                                      
cACGTTTCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGt                                                                       >  1:2072150/1‑71 (MQ=255)
  cGTTTCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGc                                                                     <  1:3642944/71‑1 (MQ=255)
      tCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCg                                                                   >  1:3818702/1‑69 (MQ=255)
      tCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCg                                                                   >  1:3060868/1‑69 (MQ=255)
      tCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGc                                                                  <  1:1063035/70‑1 (MQ=255)
       cGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCa                                                                 <  1:951672/70‑1 (MQ=255)
       cGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCa                                                                 <  1:3689329/70‑1 (MQ=255)
          aCGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGc                                                               >  1:1411171/1‑69 (MQ=255)
          aCGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCa                                                             <  1:3615860/71‑1 (MQ=255)
           cGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGc                                                               >  1:2025529/1‑68 (MQ=255)
              aTCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGt                                                         <  1:2928312/71‑1 (MQ=255)
              aTCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGt                                                         >  1:1361330/1‑71 (MQ=255)
               tCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGtt                                                        <  1:129749/71‑1 (MQ=255)
                cGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGttt                                                       >  1:2963903/1‑71 (MQ=255)
                 ggCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                                      <  1:7937/71‑1 (MQ=255)
                 ggCGCATCTGGCGGTACGATCAGAGTACGGTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                                      <  1:4131484/71‑1 (MQ=255)
                  gcgcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGttt                                                       <  1:4265981/69‑1 (MQ=255)
                  gcgcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCg                                                     <  1:3573889/71‑1 (MQ=255)
                  gcgcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTc                                                      <  1:1986706/70‑1 (MQ=255)
                   cgcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                                      >  1:1611055/1‑69 (MQ=255)
                    gcATCTGGCGGTACGATCAGAGTGCGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                                      >  1:2851171/1‑68 (MQ=255)
                    gcATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCgag                                                   <  1:3451214/71‑1 (MQ=255)
                     cATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCgaga                                                  <  1:4470276/71‑1 (MQ=255)
                      aTCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                                      >  1:3009633/1‑66 (MQ=255)
                      aTCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGAt                                                 <  1:2289206/71‑1 (MQ=255)
                      aTCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGAt                                                 <  1:4113275/71‑1 (MQ=255)
                      aTCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGAt                                                 <  1:3490903/71‑1 (MQ=255)
                       tCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATc                                                >  1:2766698/1‑71 (MQ=255)
                         tGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGAt                                                 >  1:481841/1‑68 (MQ=255)
                            cGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGct                                           >  1:2661144/1‑71 (MQ=255)
                              gTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCgag                                                   <  1:3318617/61‑1 (MQ=255)
                              gTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGctct                                         <  1:4004977/71‑1 (MQ=255)
                                 cGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCa                                                             >  1:3441755/1‑48 (MQ=255)
                                     cAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCtt                                        >  1:2201408/1‑65 (MQ=255)
                                     cAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTc                                                      >  1:1041948/1‑51 (MQ=255)
                                     cAGAGTACGTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCtt                                  >  1:3878442/1‑71 (MQ=255)
                                      agagTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTc                                 <  1:2538561/71‑1 (MQ=255)
                                       gagTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTca                                <  1:1654352/71‑1 (MQ=255)
                                          tACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTc                                                      <  1:897684/46‑1 (MQ=255)
                                            cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATcc                                               >  1:3385347/1‑51 (MQ=255)
                                            cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGt                           <  1:1738597/71‑1 (MQ=255)
                                            cGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGt                           >  1:268306/1‑71 (MQ=255)
                                             gTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTc                          >  1:2481699/1‑71 (MQ=255)
                                             gTTCACCCTGTGCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTc                          <  1:2102535/71‑1 (MQ=255)
                                              ttCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCg                         >  1:2209620/1‑71 (MQ=255)
                                               tCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCAc                                     >  1:2309507/1‑58 (MQ=255)
                                               tCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCgg                        >  1:4140609/1‑71 (MQ=255)
                                                 aCCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCt                      >  1:4020296/1‑71 (MQ=255)
                                                    cTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCg                                                     >  1:3839737/1‑37 (MQ=255)
                                                    cTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGaa                   >  1:2237510/1‑71 (MQ=255)
                                                    cTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGaa                   <  1:3267114/71‑1 (MQ=255)
                                                       tgCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAttt                >  1:1960113/1‑71 (MQ=255)
                                                       tgCCATTTTCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAt                  <  1:4599823/69‑1 (MQ=255)
                                                          cATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAAt                  <  1:4143416/66‑1 (MQ=255)
                                                           aTTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCtt                                        >  1:3685470/1‑43 (MQ=255)
                                                             tttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCt            >  1:2280440/1‑69 (MQ=255)
                                                             tttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCt            >  1:2097308/1‑69 (MQ=255)
                                                             tttCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCt            >  1:1506903/1‑69 (MQ=255)
                                                             tttCAGCAATGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCt            >  1:3536038/1‑69 (MQ=255)
                                                                     gTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTCAGCAGTgcg  <  1:2191876/71‑1 (MQ=255)
                                                                     |                                                                      
CACGTTTCGGACGCATCGGCGCATCTGGCGGTACGATCAGAGTACGTTCACCCTGTGCCATTTTCAGCAGTGCCGCAGCCAGAGTTTCGAGATCCAGCTCTTCACCTTCAGCAGTCGGCTGAATTTTGCTCAGCAGTGCG  >  W3110S.gb/3306365‑3306504

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