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 R2 260 44.3 3360226 90.5% 3041004 64.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,794,102 G→A 48.1% L398L (TTG→TTA)  gabP → gamma‑aminobutyrate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,794,1020GA48.1% 8.3 / 114.3 82L398L (TTG→TTA) gabPgamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand):  ref base G (13/29);  new base A (18/21);  total (31/51)
Fisher's exact test for biased strand distribution p-value = 1.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTT  >  W3110S.gb/2794035‑2794155
                                                                    |                                                     
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCg                                                     <  1:1346851/70‑1 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCg                                                     <  1:1362331/70‑1 (MQ=255)
taGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCg                                                     <  1:3077797/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:3157199/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:3337477/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:3031360/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:693704/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:1499239/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:2384428/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:2635583/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGaa                                                   <  1:2549683/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:2679970/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:2060722/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:1927517/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:692963/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:1691318/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:258576/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:5755/70‑1 (MQ=255)
  gTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGaa                                                   <  1:1107399/70‑1 (MQ=255)
   tCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCg                                                     <  1:332592/67‑1 (MQ=255)
   tCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCg                                                     <  1:72752/67‑1 (MQ=255)
   tCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCg                                                     <  1:1935699/67‑1 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:2450257/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:2647429/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:930859/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:1402680/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:1460402/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:3259259/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:2832988/1‑71 (MQ=255)
        gCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            >  1:2207281/1‑71 (MQ=255)
        gCCGATTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAAtg                                                 >  1:2630336/1‑66 (MQ=255)
              tCACCGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:345275/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:2386863/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:1338652/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:1470329/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:402431/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:332400/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:197439/1‑71 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATc                                       >  1:2868238/1‑70 (MQ=255)
              tCACAGTTGCGGATGCGCAAAATTATGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCTTTATcc                                      >  1:469529/1‑71 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            <  1:1604409/59‑1 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            <  1:2566747/59‑1 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            <  1:2512347/59‑1 (MQ=255)
                    ttGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            <  1:2210573/59‑1 (MQ=255)
                     tGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTACGAATGTGGCt                                            <  1:777913/58‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGTTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:3261658/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:3131632/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:298945/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:3269428/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:1962265/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:461082/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2843803/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2789006/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:1527553/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2519059/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2493084/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2302798/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:1941034/71‑1 (MQ=255)
                       cGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2092322/71‑1 (MQ=255)
                        ggATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCAc                             <  1:2943954/70‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTTCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:2663747/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:501741/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:613355/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:702201/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:1328480/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:2890043/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:1385132/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:2619519/71‑1 (MQ=255)
                                          gAGCAGAAGGAAGCGAAAATTCGCTTACGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCtt           <  1:2442269/71‑1 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTttatta      >  1:2903609/1‑67 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTttatta      >  1:2730738/1‑67 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTttatta      >  1:1554576/1‑67 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:626617/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:968472/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:858839/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:1705052/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:2112162/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:3086882/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:286545/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:2881848/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCtt  >  1:3018197/1‑71 (MQ=255)
                                                  ggaagCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCAGGCTAGTCATCGGCTTTATTACCtt  >  1:1907640/1‑71 (MQ=255)
                                                                    |                                                     
TAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCG‑AAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTT  >  W3110S.gb/2794035‑2794155

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