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 330,092 A→G 10.1% N469S (AAC→AGC)  betT → choline transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb330,0920AG10.1% 180.7 / 12.4 69N469S (AAC→AGC) betTcholine transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base A (38/24);  new base G (3/4);  total (41/28)
Fisher's exact test for biased strand distribution p-value = 4.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01

CGGCTGGCTGCGCGTCTTCTGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGT  >  W3110S.gb/330027‑330161
                                                                 |                                                                     
cGGCTGGCTGCGCGTCTTCTGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGa                                                                  >  1:2924922/1‑71 (MQ=255)
cGGCTGGCTGCGCGTCTTCTGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGa                                                                  >  1:1835826/1‑71 (MQ=255)
  gctgtctgCGCGTCTTCTGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAGCGGGata                                                                <  1:2339088/71‑1 (MQ=255)
   ctggctgCGCGTCTTCTGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAGCGGGata                                                                <  1:1460070/70‑1 (MQ=255)
              tcttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGat                                                                 <  1:4965660/58‑1 (MQ=255)
              tcttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGat                                                                 <  1:3653136/58‑1 (MQ=255)
              tcttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGat                                                                 <  1:5116791/58‑1 (MQ=255)
              tcttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaa                                                    <  1:5106750/71‑1 (MQ=255)
               cttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaa                                                    >  1:898861/1‑70 (MQ=255)
               cttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaa                                                    >  1:4924161/1‑70 (MQ=255)
               cttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaa                                                    >  1:1526735/1‑70 (MQ=255)
                ttctGGTTGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaaaa                                                  >  1:3133951/1‑71 (MQ=255)
                ttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAGCGGGATATCCGCGCTGCaaaa                                                  >  1:1938616/1‑71 (MQ=255)
                ttctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGatat                                                               >  1:848404/1‑58 (MQ=255)
                 tctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaaaa                                                  >  1:3024220/1‑70 (MQ=255)
                  ctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaaaa                                                  <  1:276323/69‑1 (MQ=255)
                  ctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaaaa                                                  <  1:2609937/69‑1 (MQ=255)
                  ctGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaaaa                                                  >  1:915596/1‑69 (MQ=255)
                   tGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCgcgc                                                         >  1:4318502/1‑61 (MQ=255)
                       cGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACg                                           >  1:4984309/1‑71 (MQ=255)
                        ggTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATc                                                              <  1:1592853/51‑1 (MQ=255)
                          tGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCaa                                                    <  1:3887684/59‑1 (MQ=255)
                          tGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGt                                         >  1:2501163/1‑70 (MQ=255)
                            gCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGAt                                      <  1:1002311/71‑1 (MQ=255)
                             cGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAGCGGGATATCCGCGCTGCAAAACACCACGGTGa                                       <  1:3711131/69‑1 (MQ=255)
                                ttGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATg                                  >  1:4420319/1‑71 (MQ=255)
                                 tGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATgg                                 >  1:1791775/1‑71 (MQ=255)
                                 tGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATgg                                 >  1:1672833/1‑71 (MQ=255)
                                 tGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATgg                                 >  1:3065143/1‑71 (MQ=255)
                                 tGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATgg                                 >  1:1298398/1‑71 (MQ=255)
                                  ggCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAac                                                 >  1:1129886/1‑54 (MQ=255)
                                   gCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATggg                                <  1:2927228/70‑1 (MQ=255)
                                   gCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATggg                                <  1:4068738/70‑1 (MQ=255)
                                   gCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATggg                                <  1:3808144/70‑1 (MQ=255)
                                     ctgctgACGCTCTGCATGCTGATGACTAGCGGGATATCCGCGCTGCAAAACACCACGGTGa                                       <  1:948929/61‑1 (MQ=255)
                                      tgctgcCGCTCGGCATGCTGATGACTCGCGGGATATCCGCGCTGCAAAACACCACg                                           >  1:2712053/1‑56 (MQ=38)
                                      tgctgACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAaca                                                <  1:3225911/51‑1 (MQ=255)
                                      tgctgACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGa                                       >  1:652275/1‑60 (MQ=255)
                                       gctgACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGc                           >  1:2143127/1‑71 (MQ=255)
                                       gctgACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGc                           >  1:2978430/1‑71 (MQ=255)
                                         tgACGCTCGGCATGCTGATGACTAACGGGATATcc                                                             <  1:2315220/35‑1 (MQ=255)
                                           aCGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGc                                                      <  1:2225468/40‑1 (MQ=255)
                                               tCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGc                              >  1:1346112/1‑60 (MQ=255)
                                                  gCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGa                                       <  1:3528516/48‑1 (MQ=255)
                                                  gCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      <  1:498865/65‑1 (MQ=255)
                                                  gCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      <  1:4856152/65‑1 (MQ=255)
                                                  gCATGCTGATGACTAACGGGATATCCGAGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      <  1:1572894/65‑1 (MQ=255)
                                                   cATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGa                                       <  1:5136570/47‑1 (MQ=255)
                                                    aTGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGa                                       >  1:640192/1‑46 (MQ=255)
                                                    aTGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGa                                       >  1:4314281/1‑46 (MQ=255)
                                                    aTGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGAtt                                     >  1:629944/1‑48 (MQ=255)
                                                    aTGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTtg               >  1:3370340/1‑70 (MQ=255)
                                                     tGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTtgtg             <  1:3609151/71‑1 (MQ=255)
                                                      gCTGATGACTAACGGGATATCGGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      >  1:994876/1‑61 (MQ=255)
                                                      gCTGATGACTAACGGGATATCGGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      >  1:988807/1‑61 (MQ=255)
                                                      gCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      >  1:4696671/1‑61 (MQ=255)
                                                      gCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTc                      >  1:3030795/1‑61 (MQ=255)
                                                       cTGATGACTAGCGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGAt           >  1:2914038/1‑71 (MQ=255)
                                                       cTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGAtt                                     >  1:1235657/1‑45 (MQ=255)
                                                       cTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGAtt                                     >  1:1963178/1‑45 (MQ=255)
                                                       cTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGAt           >  1:4853154/1‑71 (MQ=255)
                                                         gatgaCTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGAtct         >  1:2339667/1‑71 (MQ=255)
                                                          atgaCTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGAtc          <  1:243587/69‑1 (MQ=255)
                                                           tgaCTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCg                         <  1:5128455/53‑1 (MQ=255)
                                                            gaCTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATg                                  >  1:4630849/1‑43 (MQ=255)
                                                            gaCTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGAtcttct      >  1:2431254/1‑71 (MQ=255)
                                                             aCTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATg                                  >  1:3905013/1‑42 (MQ=255)
                                                               tAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGAtcttc       <  1:1714062/67‑1 (MQ=255)
                                                               tAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCg   >  1:4595295/1‑71 (MQ=255)
                                                                aaCGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGt  >  1:4558987/1‑71 (MQ=255)
                                                                aaCGGGATATCCGCGCTGCAAAACACAACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGt  >  1:3433511/1‑71 (MQ=255)
                                                                 aCGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGt  <  1:1358651/70‑1 (MQ=255)
                                                                 aCGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGt  <  1:2681546/70‑1 (MQ=255)
                                                                 aCGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGt  <  1:2934057/70‑1 (MQ=255)
                                                                 aCGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTCCTTCGt  <  1:2341/70‑1 (MQ=255)
                                                                 |                                                                     
CGGCTGGCTGCGCGTCTTCTGGTCGGTGGCGATTGGCCTGCTGACGCTCGGCATGCTGATGACTAACGGGATATCCGCGCTGCAAAACACCACGGTGATTATGGGGCTGCCGTTCAGCTTTGTGATCTTCTTCGT  >  W3110S.gb/330027‑330161

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