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 1,389,366 A→G 46.1% L311L (TTA→TTG)  tyrR → DNA‑binding transcriptional dual regulator, tyrosine‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,389,3660AG46.1% 11.4 / 108.6 76L311L (TTA→TTG) tyrRDNA‑binding transcriptional dual regulator, tyrosine‑binding
Reads supporting (aligned to +/- strand):  ref base A (18/23);  new base G (22/13);  total (40/36)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGCGAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGATGT  >  W3110S.gb/1389299‑1389431
                                                                   |                                                                 
aGGCGAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTg                                                                <  1:46778/71‑1 (MQ=255)
   cGAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGt                                                             <  1:1056494/71‑1 (MQ=255)
   cGAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGt                                                             <  1:232284/71‑1 (MQ=255)
   cGAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGt                                                             >  1:3276450/1‑71 (MQ=255)
    gAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGtt                                                            >  1:4737926/1‑71 (MQ=255)
    gAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGtt                                                            >  1:3311409/1‑71 (MQ=255)
    gAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGtt                                                            >  1:1722107/1‑71 (MQ=255)
     aaCGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGttt                                                           >  1:3081933/1‑71 (MQ=255)
     aaCGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGttt                                                           >  1:1762269/1‑71 (MQ=255)
           ggtTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTa                                                      <  1:1853225/70‑1 (MQ=255)
           ggtTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTa                                                      <  1:550610/70‑1 (MQ=255)
                  tGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGc                                              <  1:3962540/71‑1 (MQ=255)
                   gCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTaa                                                     >  1:1129293/1‑63 (MQ=255)
                        tGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTc                                        >  1:4293712/1‑71 (MQ=255)
                        tGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTc                                        >  1:1408094/1‑71 (MQ=255)
                        tGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTc                                        >  1:1727621/1‑71 (MQ=255)
                         ggATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTcc                                       >  1:3551385/1‑71 (MQ=255)
                         ggATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAat                                                    <  1:4881245/58‑1 (MQ=255)
                          gATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAat                                                    <  1:4997832/57‑1 (MQ=255)
                          gATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTcc                                       <  1:434395/70‑1 (MQ=255)
                            tGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTc                                    >  1:3343472/1‑71 (MQ=255)
                             gAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAatgatg                                                >  1:1465533/1‑58 (MQ=255)
                             gAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAatgatg                                                >  1:3498098/1‑58 (MQ=255)
                             gAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAatgatg                                                >  1:2545562/1‑58 (MQ=255)
                              aaaTAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCgg                                  <  1:1406829/71‑1 (MQ=255)
                               aaTAGGGGAAATGTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCgg                                  <  1:182659/70‑1 (MQ=255)
                               aaTAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTcc                                                         <  1:2396065/47‑1 (MQ=255)
                               aaTAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCgg                                  <  1:1570647/70‑1 (MQ=255)
                                     ggAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCg                           <  1:504418/71‑1 (MQ=255)
                                     ggAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCg                           <  1:4889103/71‑1 (MQ=255)
                                     ggAAATGTCACCACGGATGCAGGCGAAATTACTGCCTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCg                           <  1:2907910/71‑1 (MQ=255)
                                          tGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCg                           <  1:139120/66‑1 (MQ=255)
                                          tGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATAGCACTTTCCGTCGGGTTGGCg                           <  1:1273983/66‑1 (MQ=255)
                                           gTCACCACGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTcc                                       >  1:848967/1‑53 (MQ=255)
                                           gTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAatga                                                  <  1:2956182/42‑1 (MQ=255)
                                           gTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTACCGt                                     >  1:1063636/1‑55 (MQ=255)
                                            tCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAat                                                    <  1:2053734/39‑1 (MQ=255)
                                              accacGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCAt                   >  1:1815718/1‑70 (MQ=255)
                                              accacGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCAt                   >  1:161748/1‑70 (MQ=255)
                                              accacGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCAt                   >  1:1914428/1‑70 (MQ=255)
                                              accacGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATg                  <  1:4066727/71‑1 (MQ=255)
                                              accacGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATg                  <  1:3461156/71‑1 (MQ=255)
                                               ccacGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGa                 <  1:4339444/71‑1 (MQ=255)
                                                cacGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAg                >  1:1979938/1‑71 (MQ=255)
                                                cacGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAg                >  1:3443480/1‑71 (MQ=255)
                                                  cGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGt              >  1:1539090/1‑71 (MQ=255)
                                                  cGGATGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGt              >  1:1449975/1‑71 (MQ=255)
                                                  cGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGt              >  1:4915470/1‑71 (MQ=255)
                                                  cGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGt              >  1:759204/1‑71 (MQ=255)
                                                  cGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGt              >  1:912997/1‑71 (MQ=255)
                                                      tGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCAt                   <  1:1031206/62‑1 (MQ=255)
                                                      tGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCAt                   <  1:3203194/62‑1 (MQ=255)
                                                      tGCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCAt          <  1:320081/71‑1 (MQ=255)
                                                       gCAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATg         >  1:458212/1‑71 (MQ=255)
                                                        cAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGa                 >  1:111140/1‑62 (MQ=255)
                                                        cAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATg         >  1:3988663/1‑70 (MQ=255)
                                                        cAGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGt        >  1:3817458/1‑71 (MQ=255)
                                                        cAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATg         >  1:2588146/1‑70 (MQ=255)
                                                         aGGCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTc       <  1:2099761/71‑1 (MQ=255)
                                                           gCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCa                    >  1:790890/1‑56 (MQ=255)
                                                           gCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCg      <  1:1982797/70‑1 (MQ=255)
                                                           gCGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCg      <  1:3982674/70‑1 (MQ=255)
                                                           gCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGAc                      <  1:367341/54‑1 (MQ=255)
                                                            cGAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGa     >  1:3696159/1‑70 (MQ=255)
                                                            cGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGAt    >  1:2083286/1‑71 (MQ=255)
                                                             gAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGAt    >  1:1553017/1‑70 (MQ=255)
                                                             gAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGAt    >  1:2905639/1‑70 (MQ=255)
                                                             gAAATTGCTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGAt    >  1:4293346/1‑70 (MQ=255)
                                                              aaaTTACTGCGTTTCCTTAATGATGGCACTTTCCGt                                     <  1:83990/36‑1 (MQ=255)
                                                              aaaTTACTGCGTTTCCTTAATGATGGCACTTTCCGt                                     <  1:3298469/36‑1 (MQ=255)
                                                              aaaTTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCAt                   <  1:613691/54‑1 (MQ=255)
                                                              aaaTTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGTATGTCGAtgt  <  1:1524809/71‑1 (MQ=255)
                                                              aaaTTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGAtgt  <  1:4168020/71‑1 (MQ=255)
                                                               aaTTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGAtg   >  1:2747831/1‑69 (MQ=255)
                                                                aTTACTGCGTTTCCTTAATGATGGCACTTTCCGTCg                                   >  1:2647319/1‑36 (MQ=255)
                                                                 ttACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGc            <  1:2233335/58‑1 (MQ=255)
                                                                   |                                                                 
AGGCGAACGGTGGTTCGGTGCTGTTGGATGAAATAGGGGAAATGTCACCACGGATGCAGGCGAAATTACTGCGTTTCCTTAATGATGGCACTTTCCGTCGGGTTGGCGAAGACCATGAGGTGCATGTCGATGT  >  W3110S.gb/1389299‑1389431

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