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 1,557,824 C→T 7.0% Q57Q (CAG→CAA)  bdm ← biofilm‑dependent modulation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,557,8240CT 7.0% 267.6 / 7.6 86Q57Q (CAG→CAA) bdmbiofilm‑dependent modulation protein
Reads supporting (aligned to +/- strand):  ref base C (47/31);  new base T (2/4);  total (50/36)
Fisher's exact test for biased strand distribution p-value = 2.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.26e-01

TAGGTTGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGT  >  W3110S.gb/1557754‑1557891
                                                                      |                                                                   
tAGGTTGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGc                                                                     >  1:1193629/1‑71 (MQ=255)
      gCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGTTa                                                                <  1:3916379/70‑1 (MQ=255)
       ccGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGa                                                              <  1:869301/71‑1 (MQ=255)
          aTCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           <  1:2528619/71‑1 (MQ=255)
          aTCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           >  1:968733/1‑71 (MQ=255)
          aTCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           <  1:2714419/71‑1 (MQ=255)
           tCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           >  1:339461/1‑70 (MQ=255)
           tCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGatat                                                           >  1:1557693/1‑70 (MQ=255)
            cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGa                                                              >  1:1974823/1‑66 (MQ=255)
            cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATc                                                          >  1:903637/1‑70 (MQ=255)
            cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:758217/1‑71 (MQ=255)
            cAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:846257/1‑71 (MQ=255)
               gCATAGCACCTTAAAGCGTAGGGTGCTTGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      <  1:90555/71‑1 (MQ=255)
                cATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGc                                                                     >  1:1728772/1‑55 (MQ=255)
                 aTAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAg                                                    >  1:2251054/1‑71 (MQ=255)
                  tAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGat                                                             <  1:3522663/61‑1 (MQ=255)
                   aGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                <  1:3664488/57‑1 (MQ=255)
                    gCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:3280156/1‑56 (MQ=255)
                    gCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:2043113/1‑63 (MQ=255)
                    gCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGAt                                                 >  1:2251613/1‑71 (MQ=255)
                       ccatAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACt                                                       >  1:1225459/4‑62 (MQ=255)
                       ccTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCa                                                         >  1:671177/1‑60 (MQ=255)
                         ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:787990/1‑58 (MQ=255)
                         ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      >  1:3493044/1‑61 (MQ=255)
                         ttAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      >  1:4417125/1‑61 (MQ=255)
                          tAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:1438350/1‑50 (MQ=255)
                          tAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAgg                                                   >  1:1662658/1‑63 (MQ=255)
                           aaaGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGa                                                     >  1:3579858/1‑60 (MQ=255)
                           aaaGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTa                                          >  1:4415843/1‑71 (MQ=255)
                            aaGCGTAGTGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTAt                                         <  1:2179271/71‑1 (MQ=255)
                            aaGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTAt                                         <  1:174432/71‑1 (MQ=255)
                                gTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCa                                                         >  1:2516718/1‑51 (MQ=255)
                                gTACGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGa                                     <  1:2872458/71‑1 (MQ=255)
                                   gggTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGt                                                                 >  1:3105240/1‑40 (MQ=255)
                                    ggTGCTGGCCACTGACCAGATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGtt                                           <  1:1252462/61‑1 (MQ=255)
                                    ggTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGa                                                              <  1:1810558/42‑1 (MQ=255)
                                    ggTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCt                                 >  1:2940593/1‑71 (MQ=255)
                                    ggTGCTGGCCACTGACCACATAATTGATCGTTTGATGGTAGATATCACTGAGGATGTCGTTATCAGAAGCt                                 >  1:907730/1‑71 (MQ=255)
                                     gTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGa                                                              >  1:2357226/1‑41 (MQ=255)
                                     gTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      <  1:915168/49‑1 (MQ=255)
                                     gTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      <  1:3414059/49‑1 (MQ=255)
                                     gTGCTGGCCACTGACCACATAATTGATCGTTTG‑TTGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTc                               <  1:4129607/71‑1 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCtt                                >  1:2467378/1‑70 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTc                               <  1:1981369/71‑1 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                <  1:298073/38‑1 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGaa                                    <  1:2539838/66‑1 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTc                               <  1:1004297/71‑1 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTc                               <  1:1565592/71‑1 (MQ=255)
                                      tGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTc                               <  1:3180764/71‑1 (MQ=255)
                                       gCTGGCCACTGACCACATAATTGATCGTTTGCTGGTa                                                                >  1:2566562/1‑37 (MQ=255)
                                        cTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGa                                                              >  1:845900/1‑38 (MQ=255)
                                         tGGCCACTGACCACATAATTGATCGTTTGCTGGTAGat                                                             <  1:281858/38‑1 (MQ=255)
                                            ccACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCa                         >  1:1407171/1‑71 (MQ=255)
                                            ccACTGACCACATAATTAATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAAccc                          <  1:1164111/70‑1 (MQ=255)
                                             cACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGtt                                           <  1:3649310/52‑1 (MQ=255)
                                               cTGATCACATAATTGATCGTTTGCTGGTAGATATCACTGAg                                                    <  1:3330216/41‑1 (MQ=255)
                                                tGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGa                                                  >  1:3206392/1‑42 (MQ=255)
                                                tGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCa                                       <  1:2176412/53‑1 (MQ=255)
                                                tGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCa                         >  1:250330/1‑67 (MQ=255)
                                                tGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCa                         >  1:4412369/1‑67 (MQ=255)
                                                 gACCACATAATTGATCGTTTGCTGGTAGATATCACTg                                                      >  1:32389/1‑37 (MQ=255)
                                                 gACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCa                              >  1:819761/1‑61 (MQ=255)
                                                 gACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTgg                    >  1:548587/1‑71 (MQ=255)
                                                  aCCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTAt                                         >  1:787238/1‑49 (MQ=255)
                                                   ccACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCa                                       >  1:479999/1‑50 (MQ=255)
                                                   ccACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCa                                       >  1:1243106/1‑50 (MQ=255)
                                                   ccACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTc                  <  1:442428/71‑1 (MQ=255)
                                                    cacaTAATTGATCGTTTGCTGGTAGATATCACTGa                                                     <  1:1622171/35‑1 (MQ=255)
                                                    cacaTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTa                                          <  1:4416200/46‑1 (MQ=255)
                                                    cacaTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGt                   >  1:1448537/1‑69 (MQ=255)
                                                    cacaTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGt                   >  1:1977395/1‑69 (MQ=255)
                                                      caTAATTGATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGa                                     <  1:992898/49‑1 (MQ=255)
                                                      caTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGc               >  1:2655609/1‑71 (MQ=255)
                                                      caTAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGc               >  1:1037071/1‑71 (MQ=255)
                                                        tAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCa                                       >  1:1769357/1‑45 (MQ=255)
                                                        tAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTc             >  1:4515927/1‑71 (MQ=255)
                                                         aaTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCt              >  1:228661/1‑69 (MQ=255)
                                                          aTTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCa           >  1:441151/1‑71 (MQ=255)
                                                            tGATCGTTTGCTTGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCAt          <  1:1896071/70‑1 (MQ=255)
                                                             gATCGTTTGTTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCAt          <  1:1813834/69‑1 (MQ=255)
                                                              aTCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAAccc                          <  1:2744983/52‑1 (MQ=255)
                                                              aTCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       <  1:1859740/71‑1 (MQ=255)
                                                              aTCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATga        <  1:1629981/70‑1 (MQ=255)
                                                               tCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       >  1:4047035/1‑70 (MQ=255)
                                                               tCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATgag       >  1:3447130/1‑70 (MQ=255)
                                                                cGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCAt                        >  1:4473976/1‑52 (MQ=255)
                                                                 gTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCCTCAACCCATTTGGTCAGCTCCATGAGAAt    <  1:539498/71‑1 (MQ=255)
                                                                    tGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGt  >  1:2285811/1‑70 (MQ=255)
                                                                      |                                                                   
TAGGTTGCCGATCAAGCATAGCACCTTAAAGCGTAGGGTGCTGGCCACTGACCACATAATTGATCGTTTGCTGGTAGATATCACTGAGGATGTCGTTATCAGAAGCTTCAACCCATTTGGTCAGCTCCATGAGAATGT  >  W3110S.gb/1557754‑1557891

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