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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,418,872 A→G 36.6% *388* (TAA→TGA)  yjfC → predicted synthetase/amidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,418,8720AG36.6% 132.5 / 159.6 146*388* (TAA→TGA) yjfCpredicted synthetase/amidase
Reads supporting (aligned to +/- strand):  ref base A (41/51);  new base G (36/17);  total (77/69)
Fisher's exact test for biased strand distribution p-value = 9.31e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.12e-01

Only 100 of 150 total aligned reads displayed.

GATCCGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCATT  >  W3110S.gb/4418804‑4418940
                                                                    |                                                                    
gATCCGTGAACATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAg                                                                    <  1:1286165/71‑1 (MQ=255)
 aTCCGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATgaga                                                                   <  1:4377134/71‑1 (MQ=255)
   ccGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAAt                                                                 >  1:4856688/1‑71 (MQ=255)
   ccGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAAt                                                                 >  1:3668015/1‑71 (MQ=255)
   ccGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAAt                                                                 >  1:825829/1‑71 (MQ=255)
   ccGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAAt                                                                 >  1:1586853/1‑71 (MQ=255)
    cGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATg                                                                >  1:3394875/1‑71 (MQ=255)
     gTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGt                                                               <  1:3397986/71‑1 (MQ=255)
       gAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGttt                                                             >  1:3336596/1‑71 (MQ=255)
       gAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGttt                                                             >  1:4382327/1‑71 (MQ=255)
        aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTCGATAAGAATGttt                                                             >  1:3249486/1‑70 (MQ=255)
          gATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAg                                                          >  1:3502489/1‑71 (MQ=255)
           aTAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAg                                                          >  1:789077/1‑70 (MQ=255)
            tAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCa                                                        <  1:4568727/71‑1 (MQ=255)
             aaCACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCaa                                                       >  1:1406595/1‑71 (MQ=255)
               cacacTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtc                                                     >  1:2489593/1‑71 (MQ=255)
               cacacTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtc                                                     >  1:3707294/1‑71 (MQ=255)
               cacacTGATCAACAAAGACACCTCACGTTACGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtc                                                     >  1:1131600/1‑71 (MQ=255)
                   cTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAg                                                                    <  1:973557/52‑1 (MQ=255)
                   cTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCtt                                                 >  1:3796259/1‑71 (MQ=255)
                    tGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCttt                                                >  1:3894164/1‑71 (MQ=255)
                    tGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCaa                                                       <  1:2923880/64‑1 (MQ=255)
                       tCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTg                                             >  1:2636401/1‑71 (MQ=255)
                        cACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGt                                            >  1:3038629/1‑71 (MQ=255)
                         aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGt                                                               >  1:2767032/1‑51 (MQ=255)
                         aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:2698149/70‑1 (MQ=255)
                         aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:2598046/70‑1 (MQ=255)
                         aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:2494445/70‑1 (MQ=255)
                         aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:1900931/70‑1 (MQ=255)
                          ccAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCa                                          >  1:12809/1‑71 (MQ=255)
                             aaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGa                                       <  1:4343191/71‑1 (MQ=255)
                             aaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATg                                        >  1:1441641/1‑70 (MQ=255)
                               gACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAAt                                     >  1:4952594/1‑71 (MQ=255)
                                acacCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATc                                    >  1:3535483/1‑71 (MQ=255)
                                   ccTCACGTTTCGTTCCGCATTACATTGCTGGATgaga                                                                   <  1:2096657/37‑1 (MQ=255)
                                   ccTCACGTTTCGTTCCGCATTACATTGCTGGATAAg                                                                    <  1:4770301/36‑1 (MQ=255)
                                   ccTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCAt                                 <  1:1328209/71‑1 (MQ=255)
                                    cTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTg                                             <  1:4614947/58‑1 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCa                                                        <  1:3081855/46‑1 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:2470045/1‑71 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCa                                                        <  1:4708520/46‑1 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCa                                                        <  1:2932481/46‑1 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCa                                                        <  1:1049061/46‑1 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCa                                                        <  1:273134/46‑1 (MQ=255)
                                     tCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATg                                        <  1:4161532/62‑1 (MQ=255)
                                      cACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:1703551/1‑70 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAAt                                                      >  1:980414/1‑46 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCttt                                                >  1:4160695/1‑52 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCttt                                                >  1:3513286/1‑52 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCttt                                                >  1:1855840/1‑52 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:2158171/1‑69 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:4528610/1‑69 (MQ=255)
                                       aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGc                              <  1:1384451/70‑1 (MQ=255)
                                       aCGTTTCGATCCGCATTACATTGCTGGATAAGAATGTTTTAGCaa                                                       >  1:1472573/1‑45 (MQ=255)
                                        cGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAg                            >  1:2292261/1‑71 (MQ=255)
                                         gTTTCGTTCCGCATTACATTGCTGGATAAGAATGtttt                                                            <  1:2354759/38‑1 (MQ=255)
                                         gTTTCGTTCCGCATTACATTGCTGGATAAGAATGtttt                                                            <  1:2203895/38‑1 (MQ=255)
                                         gTTTCGTTCCGCATTACATTGCTGGATAAGAATGtttt                                                            <  1:564788/38‑1 (MQ=255)
                                         gTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTc                                               >  1:1583278/1‑51 (MQ=255)
                                         gTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGt                           <  1:98419/71‑1 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTg                          <  1:3894735/71‑1 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             <  1:2723595/36‑1 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             <  1:399176/36‑1 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             <  1:2432984/36‑1 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGc                                                         <  1:4290050/40‑1 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGt                           >  1:1301372/1‑70 (MQ=255)
                                          tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGt                           >  1:4709313/1‑70 (MQ=255)
                                           ttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGa                         >  1:1966893/1‑71 (MQ=255)
                                           ttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGa                         >  1:711000/1‑71 (MQ=255)
                                           ttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGa                         >  1:1953891/1‑71 (MQ=255)
                                            tCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCAt                                         >  1:97637/1‑54 (MQ=255)
                                            tCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGAc                        >  1:928904/1‑71 (MQ=255)
                                            tCGTTCCGCATTACATTGCTGGATAAGAATGTTTTa                                                           >  1:2173697/1‑36 (MQ=255)
                                             cGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTg                                             >  1:3447757/1‑49 (MQ=255)
                                             agTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGAc                        >  1:5040744/2‑70 (MQ=255)
                                              gTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCaa                                                       >  1:807282/1‑38 (MQ=255)
                                              gTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCaa                                                       >  1:5018590/1‑38 (MQ=255)
                                              gTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      <  1:1205062/71‑1 (MQ=255)
                                              gTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      <  1:3658766/71‑1 (MQ=255)
                                               ttCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATg                                        <  1:3038661/52‑1 (MQ=255)
                                               ttCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      <  1:2362686/70‑1 (MQ=255)
                                                 ccGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATAc                   >  1:1879012/1‑71 (MQ=255)
                                                  cGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACt                  <  1:465950/71‑1 (MQ=255)
                                                  cGCATTACATTGCTGGATAAGAATGTTTTAGCAATctct                                                  <  1:40597/39‑1 (MQ=255)
                                                   gCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTa                 <  1:904902/71‑1 (MQ=255)
                                                   gCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTa                 <  1:5038637/71‑1 (MQ=255)
                                                     aTTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCAt                                         >  1:14791/1‑45 (MQ=255)
                                                      ttACATTGCTGGATGAGAATGTTTTAGCAATctct                                                  <  1:3870262/35‑1 (MQ=255)
                                                        aCATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGa                         >  1:2132761/1‑58 (MQ=255)
                                                        aCATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTaa                >  1:2829201/1‑67 (MQ=255)
                                                        aCATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGt            >  1:278997/1‑71 (MQ=255)
                                                         cATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGt            >  1:1392667/1‑70 (MQ=255)
                                                         cATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTg           <  1:3065303/71‑1 (MQ=255)
                                                           ttGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGAc         <  1:2269550/71‑1 (MQ=255)
                                                           ttGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGAc         <  1:411400/71‑1 (MQ=255)
                                                             gCTGGATAAGAATGTTTTAGCAATCTCTTTCTTTCATGAATCCATGGCAGTGACCATACTAATGGTg           <  1:2239736/67‑1 (MQ=255)
                                                              cTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGc      <  1:3895760/71‑1 (MQ=255)
                                                               tGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTg           <  1:1037045/65‑1 (MQ=255)
                                                                 gATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCAt   >  1:4018327/1‑71 (MQ=255)
                                                                   tAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCAtt  >  1:5008583/1‑70 (MQ=255)
                                                                    |                                                                    
GATCCGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCATT  >  W3110S.gb/4418804‑4418940

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