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 4,418,872 A→G 10.8% *388* (TAA→TGA)  yjfC → predicted synthetase/amidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,418,8720AG10.8% 263.6 / 22.8 102*388* (TAA→TGA) yjfCpredicted synthetase/amidase
Reads supporting (aligned to +/- strand):  ref base A (53/38);  new base G (3/8);  total (56/46)
Fisher's exact test for biased strand distribution p-value = 6.15e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.89e-01

Only 100 of 105 total aligned reads displayed.

ATCCGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCATT  >  W3110S.gb/4418805‑4418940
                                                                   |                                                                    
aTCCGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAg                                                                    >  1:2598415/1‑70 (MQ=255)
  ccGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAAt                                                                 >  1:3909737/1‑71 (MQ=255)
  ccGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAAt                                                                 >  1:2043466/1‑71 (MQ=255)
   cGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAAt                                                                 <  1:2745690/70‑1 (MQ=255)
   cGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATg                                                                >  1:682542/1‑71 (MQ=255)
    gTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGt                                                               <  1:500590/71‑1 (MQ=255)
    gTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGt                                                               <  1:4469668/71‑1 (MQ=255)
     tGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGtt                                                              >  1:4426528/1‑71 (MQ=255)
       aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGtttt                                                            <  1:3739680/71‑1 (MQ=255)
       aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGtttt                                                            <  1:2972636/71‑1 (MQ=255)
       aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             <  1:4270939/70‑1 (MQ=255)
       aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             <  1:4156613/70‑1 (MQ=255)
       aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             >  1:1721157/1‑70 (MQ=255)
       aaGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             >  1:4481407/1‑70 (MQ=255)
        aGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             >  1:1680399/1‑69 (MQ=255)
        aGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             >  1:4570344/1‑69 (MQ=255)
           tAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGc                                                         >  1:4317576/1‑70 (MQ=255)
            aaCACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCaa                                                       >  1:724589/1‑71 (MQ=255)
              cacacTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtc                                                     >  1:4245129/1‑71 (MQ=255)
               acacTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTa                                                           >  1:121076/1‑64 (MQ=255)
               acacTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtct                                                    >  1:2146442/1‑71 (MQ=255)
                 acTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATctct                                                  >  1:3146708/1‑71 (MQ=255)
                 acTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATctct                                                  >  1:1124163/1‑71 (MQ=255)
                 acTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATctct                                                  >  1:1776696/1‑71 (MQ=255)
                  cTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATctct                                                  >  1:3898847/1‑70 (MQ=255)
                   tGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCttt                                                >  1:3454617/1‑71 (MQ=255)
                    gATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATAGCTGGATAAGAATGTTTTAGCAATCTCTTTc                                               >  1:3199639/1‑71 (MQ=255)
                     aTCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCttt                                                <  1:1348076/69‑1 (MQ=255)
                     aTCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCt                                              >  1:623960/1‑71 (MQ=255)
                     aTCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCt                                              >  1:3427579/1‑71 (MQ=255)
                      tCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTg                                             >  1:2454578/1‑71 (MQ=255)
                      tCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTg                                             <  1:41566/71‑1 (MQ=255)
                      tCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTg                                             >  1:3117936/1‑71 (MQ=255)
                        aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:4219492/70‑1 (MQ=255)
                        aCCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:4358745/70‑1 (MQ=255)
                         ccAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAAt                                                                 <  1:754898/48‑1 (MQ=255)
                          cAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCAt                                         >  1:1501562/1‑71 (MQ=255)
                           aaaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCAt                                         >  1:3394734/1‑70 (MQ=255)
                            aaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATaa                                                                     <  1:3079992/41‑1 (MQ=255)
                            aaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATg                                        >  1:3443679/1‑70 (MQ=255)
                            aaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATg                                        >  1:1291932/1‑70 (MQ=255)
                            aaGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATg                                        >  1:2923745/1‑70 (MQ=255)
                              gACAACTCACGTTTCGTTCCGCATTACATTGCTGGATaa                                                                     >  1:4424881/1‑39 (MQ=255)
                                cacCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATc                                    >  1:1032632/1‑70 (MQ=255)
                                 acCTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCa                                  <  1:1363758/71‑1 (MQ=255)
                                 acCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGaa                                      <  1:3106716/67‑1 (MQ=255)
                                 acCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAAt                                     >  1:1001919/1‑68 (MQ=255)
                                  ccTCACGTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCAt                                 <  1:1042843/71‑1 (MQ=255)
                                   cTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGc                                                         <  1:3049471/46‑1 (MQ=255)
                                   cTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATg                                >  1:3382079/1‑71 (MQ=255)
                                   cTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATg                                >  1:2255869/1‑71 (MQ=255)
                                    tCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCAt                                 >  1:4116725/1‑69 (MQ=255)
                                     cACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:3785181/1‑70 (MQ=255)
                                      aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtctc                                                   >  1:3749269/1‑49 (MQ=255)
                                      aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               <  1:4068602/69‑1 (MQ=255)
                                      aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               <  1:2853026/69‑1 (MQ=255)
                                      aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:4221301/1‑69 (MQ=255)
                                      aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATg                                <  1:4085683/68‑1 (MQ=255)
                                      aCGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCa                             <  1:4301884/71‑1 (MQ=255)
                                       cGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               <  1:1128639/68‑1 (MQ=255)
                                       cGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAg                            >  1:3900741/1‑71 (MQ=255)
                                        gTTTCGTTCCGCATTACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGt                           <  1:3047508/71‑1 (MQ=255)
                                        gTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGt                           <  1:4296519/71‑1 (MQ=255)
                                         tttCGTTCCGCATTACATTGCTGGATAAGAATGttt                                                             <  1:222042/36‑1 (MQ=255)
                                         tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAg                                                          <  1:4279538/39‑1 (MQ=255)
                                         tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAg                                                          <  1:3375219/39‑1 (MQ=255)
                                         tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGt                                            <  1:1420343/53‑1 (MQ=255)
                                         tttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCAt                                 <  1:1166404/64‑1 (MQ=255)
                                          ttCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGa                         >  1:2158777/1‑71 (MQ=255)
                                           tCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAAtctc                                                   >  1:3602769/1‑44 (MQ=255)
                                           tCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCa                             >  1:2573499/1‑66 (MQ=255)
                                           tCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGAc                        >  1:2556926/1‑71 (MQ=255)
                                             gTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCttt                                                >  1:2848397/1‑45 (MQ=255)
                                             gTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      <  1:1145277/71‑1 (MQ=255)
                                             gTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      <  1:1722485/71‑1 (MQ=255)
                                               tCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATgg                               >  1:3927443/1‑60 (MQ=255)
                                                ccGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTg                          >  1:1358503/1‑64 (MQ=255)
                                                ccGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGa                         >  1:786271/1‑65 (MQ=255)
                                                ccGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATAc                   >  1:743907/1‑71 (MQ=255)
                                                ccGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATAc                   >  1:321286/1‑71 (MQ=255)
                                                ccGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATAc                   >  1:2044966/1‑71 (MQ=255)
                                                   cATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCAt                                 <  1:4415914/54‑1 (MQ=255)
                                                     ttACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTg                                             <  1:4071926/40‑1 (MQ=255)
                                                     ttACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATg              <  1:423371/71‑1 (MQ=255)
                                                      tACATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGa                                       >  1:2384842/1‑45 (MQ=255)
                                                       aCATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAAt                                     >  1:3080618/1‑46 (MQ=255)
                                                       aCATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATgg             <  1:2327810/70‑1 (MQ=255)
                                                       aCATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGt            >  1:2220700/1‑71 (MQ=255)
                                                        cATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTg           <  1:4463475/71‑1 (MQ=255)
                                                        cATTGCTGGATGAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATCGCAGTGACCATACTAATGGTg           <  1:319846/71‑1 (MQ=255)
                                                        cATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGt            <  1:853687/70‑1 (MQ=255)
                                                         aTTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGt            <  1:4525908/69‑1 (MQ=255)
                                                             cTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      >  1:3702032/1‑55 (MQ=255)
                                                               ggATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATg              <  1:3737288/61‑1 (MQ=255)
                                                                gATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCAt   >  1:398870/1‑71 (MQ=255)
                                                                 aTAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCa                      <  1:4406833/51‑1 (MQ=255)
                                                                 aTAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGAc         <  1:48320/64‑1 (MQ=255)
                                                                 aTAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGAc         <  1:1528715/64‑1 (MQ=255)
                                                                  tAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATg              >  1:811865/1‑58 (MQ=255)
                                                                  tAAGAATGTTTTAGCAATCACTTTCTGTCATGAATCCATGGCAGTGACCATACTACTGGTGACTGCCAtt  <  1:1013381/70‑1 (MQ=255)
                                                                   |                                                                    
ATCCGTGAAGATAACACACTGATCACCAAAGACACCTCACGTTTCGTTCCGCATTACATTGCTGGATAAGAATGTTTTAGCAATCTCTTTCTGTCATGAATCCATGGCAGTGACCATACTAATGGTGACTGCCATT  >  W3110S.gb/4418805‑4418940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A