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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,763,072 T→A Q246H (CAA→CAT)  yfjL ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,763,0720TA84.6% 239.9 / 34.1 91Q246H (CAA→CAT) yfjLhypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (1/13);  new base A (46/31);  total (47/44)
Fisher's exact test for biased strand distribution p-value = 2.71e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.66e-01

CGCTCTAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAGGACTTGTCAT  >  W3110S.gb/2763006‑2763136
                                                                  |                                                                
cgcTCTAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGt                                                              <  1:2895079/71‑1 (MQ=255)
cgcTCTAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGt                                                              <  1:2898807/71‑1 (MQ=255)
cgcTCTAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGt                                                              <  1:3460805/71‑1 (MQ=255)
 gcTCTAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGt                                                              <  1:2926376/70‑1 (MQ=255)
    ctAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATc                                                          >  1:2840695/1‑71 (MQ=255)
    ctAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATc                                                          >  1:3808807/1‑71 (MQ=255)
       aaaggCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1577954/68‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1074267/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1476605/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1430850/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:3726544/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:3905775/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1193226/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:109438/71‑1 (MQ=255)
       aaTGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1080809/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGTCTGACCGAGAATGGTCATCTTCGa                                                     <  1:4048439/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGTCTGACCGAGAATGGTCATCTTCGa                                                     <  1:4053243/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGGCCGAGATTGGTCATCTTc                                                       <  1:2398559/69‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:2196377/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:1997328/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:1979217/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:2450301/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:279526/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:1639274/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:2975266/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:3448428/71‑1 (MQ=255)
         tGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGa                                                     <  1:1291356/71‑1 (MQ=255)
                      tgGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGa                                         <  1:965489/70‑1 (MQ=255)
                      tgGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGa                                         <  1:2430131/70‑1 (MQ=255)
                      tgGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGa                                         <  1:3566837/70‑1 (MQ=255)
                          gTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:3726467/52‑1 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:3616720/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:964505/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:354465/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:1325711/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:3137092/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:2690718/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:16335/1‑71 (MQ=255)
                           tAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACt                                   >  1:2769219/1‑71 (MQ=255)
                            aaGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTc                                                       <  1:1225268/50‑1 (MQ=255)
                              gTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCa                                                            <  1:2949485/43‑1 (MQ=255)
                              gTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCa                                                            <  1:3709476/43‑1 (MQ=255)
                              gTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCa                                                            <  1:4068861/43‑1 (MQ=255)
                              gTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCa                                                            <  1:591085/43‑1 (MQ=255)
                               tCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               <  1:3155859/71‑1 (MQ=255)
                               tCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               <  1:86784/71‑1 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:1075965/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGaa                                        >  1:1728126/1‑60 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:2284706/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:3892056/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:3974731/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:2127908/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:315524/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:1131199/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:3609896/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:2316489/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:1504025/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:1249054/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:2640019/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:4082496/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:2697910/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:1733123/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               >  1:50163/1‑69 (MQ=255)
                                 ccGTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTT‑AACCACTCAAGTAg                            >  1:481320/1‑71 (MQ=255)
                                   gTTTGACGTAGATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAgg                           <  1:3015684/71‑1 (MQ=255)
                                             gagtttGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1767773/4‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCg                   >  1:2839733/1‑69 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:804404/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1095253/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:4066388/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3727211/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3177504/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3711333/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:2376861/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1847803/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1799714/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:2787235/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1524661/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3096239/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3133375/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1266817/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3593824/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:3715177/1‑70 (MQ=255)
                                             gATTTTGCGGCCTGACCGAGAATGGTCATCTTAGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGt                  >  1:1200039/1‑70 (MQ=255)
                                                 ttGCGGCCTGACCGAGATTGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGt              <  1:1547851/70‑1 (MQ=255)
                                                   gCGGCCTGACCGAGGATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAg            <  1:2777114/70‑1 (MQ=255)
                                                   gCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAg            <  1:1461378/70‑1 (MQ=255)
                                                   gCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAg            <  1:2387516/70‑1 (MQ=255)
                                                   gCGGCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAg            <  1:2257761/70‑1 (MQ=255)
                                                      gCCTGACCGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAg                               <  1:3122888/48‑1 (MQ=255)
                                                            ccGAGAATGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAGGACTTGtcat  <  1:820563/71‑1 (MQ=255)
                                                                  |                                                                
CGCTCTAAATGGCGTAAGGATGTGGGGTAAGTCCCGTTTGACGTAGATTTTGCGGCCTGACCGAGATTGGTCATCTTCGACACGCTGCTTGAACCACTCAAGTAGGTCTGGTCGTAAGTAGGACTTGTCAT  >  W3110S.gb/2763006‑2763136

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