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
A3 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 704,276 T→C 29.3% L123L (CTA→CTG)  ymcA ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported704,2760TC29.3% 136.5 / 66.0 92L123L (CTA→CTG) ymcAconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (33/32);  new base C (18/9);  total (51/41)
Fisher's exact test for biased strand distribution p-value = 1.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

AGATACTCACCGTCAAACAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGC  >  Exported/704214‑704343
                                                              |                                                                   
aGATACTCACCGTCAAACAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGt                                                              >  1:2073394/1‑70 (MQ=255)
    aCTCACCGTCAAACAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAAcc                                                          <  1:3380847/70‑1 (MQ=255)
     cTCACCGTCAAACAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACct                                                         <  1:1326816/70‑1 (MQ=255)
        aCCGTCAAACAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACcttctt                                                     >  1:2573815/1‑71 (MQ=255)
              aaaCAGCCCCGTACCGCCGATATCCCGCGCACCAACCGCCACTTGCGGCAGCCAGTaa                                                            >  1:3500398/1‑58 (MQ=255)
              aaaCAGCCCCGTACCGCCGATATCCCGCGCACCAACCGCCACTTGCGGCAGCCAGTaa                                                            >  1:2777041/1‑58 (MQ=255)
              aaaCAGCCCCGTACCGCCGATATCCCGCGCACCAACCGCCACTTGCGGCAGCCAGTAAct                                                          >  1:1872842/1‑59 (MQ=255)
              aaaCAGCCCCGTACCGCCGATATCCCGCGCACCAACCGCCACTTGCGGCAGCCAGTAACTCTCTTCCcac                                                >  1:497847/1‑70 (MQ=255)
              aaaCAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTaa                                                            >  1:3834859/1‑58 (MQ=255)
              aaaCAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCca                                                 >  1:3045559/1‑69 (MQ=255)
                aCAGCCCCGTACCGCCGATATCCCGCGCACCAACCGCCACTTGCGGCAGCCAGTAACTCTCTTCCca                                                 >  1:2056560/1‑67 (MQ=255)
                 cAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGc                                            >  1:2162574/1‑71 (MQ=255)
                  aGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGt                                                                     <  1:3471653/45‑1 (MQ=255)
                  aGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGt                                                                     <  1:2973130/45‑1 (MQ=255)
                        gTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGtt                                      >  1:4853548/1‑70 (MQ=255)
                          aCCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTaa                                                            >  1:3471704/1‑46 (MQ=255)
                           ccAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGt                                                              >  1:3252915/1‑43 (MQ=255)
                           ccAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGaa                                         >  1:1735024/1‑64 (MQ=255)
                            cAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCca                                                 <  1:1845524/55‑1 (MQ=255)
                            cAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaa                                  <  1:4148528/70‑1 (MQ=255)
                             aGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGaa                                         >  1:2754284/1‑62 (MQ=255)
                              gCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTGAc                                                           >  1:3648486/1‑43 (MQ=255)
                              gCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATc                               <  1:1958778/71‑1 (MQ=255)
                                  tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACcttc                                                       <  1:2170687/43‑1 (MQ=255)
                                  tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTccc                                                  <  1:4437676/48‑1 (MQ=255)
                                  tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTccc                                                  <  1:1352663/48‑1 (MQ=255)
                                  tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTccc                                                  <  1:307749/48‑1 (MQ=255)
                                  tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                           <  1:4213472/55‑1 (MQ=255)
                                  tatCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                           <  1:138198/55‑1 (MQ=255)
                                   atCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                            >  1:2059709/1‑69 (MQ=255)
                                   atCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                            >  1:4044390/1‑69 (MQ=255)
                                    tCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAAc                                                           >  1:1106530/1‑37 (MQ=255)
                                    tCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                   <  1:5641687/61‑1 (MQ=255)
                                    tCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAAt                           >  1:4654760/1‑69 (MQ=255)
                                      aCGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                >  1:2205433/1‑62 (MQ=255)
                                      aCGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAtt                       >  1:4414167/1‑71 (MQ=255)
                                      aCGTTTACCAAACGCAACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                >  1:3409610/1‑62 (MQ=255)
                                       cGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAgg                                             <  1:473230/48‑1 (MQ=255)
                                        gTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                           <  1:2419561/49‑1 (MQ=255)
                                        gTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCg                                           <  1:4828791/49‑1 (MQ=255)
                                        gTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTg                     >  1:2473338/1‑71 (MQ=255)
                                         tttACCAAACGCCACTTGCGGTAGCCAGTAACcttctt                                                     <  1:573403/38‑1 (MQ=255)
                                         tttACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGa                                          <  1:2828585/49‑1 (MQ=255)
                                          ttACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaaa                                 >  1:311831/1‑57 (MQ=255)
                                           tACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAttt                      <  1:4087923/67‑1 (MQ=255)
                                            aCCAACCGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCtt                 <  1:5372011/71‑1 (MQ=255)
                                             ccAACCGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCtt                 >  1:985316/1‑70 (MQ=255)
                                             ccAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCtt                 <  1:2763889/70‑1 (MQ=255)
                                              cAACCGCCACTTGCGGCAGCCAGTAACTCTCTTcc                                                   >  1:5032234/1‑35 (MQ=16)
                                              cAACCGCCACTTGCGGCAGCCAGTAACTCTCTTcc                                                   >  1:5094348/1‑35 (MQ=16)
                                              cAACCGCCACTTGCGGCAGCCAGTAACTCTCTTcc                                                   >  1:2937466/1‑35 (MQ=16)
                                              cAACCGCCACTTGCGGCAGCCAGTAACTCTCTTcc                                                   >  1:2131396/1‑35 (MQ=16)
                                              cAACCGCCACTTGCGGCAGCCAGTAACTCTCTTcc                                                   >  1:1365190/1‑35 (MQ=16)
                                              cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCcac                                                >  1:2383066/1‑38 (MQ=255)
                                              cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaaa                                 >  1:3623456/1‑53 (MQ=255)
                                              cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGAttt                      <  1:4834842/64‑1 (MQ=255)
                                              cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg               <  1:2303699/71‑1 (MQ=255)
                                              cAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg               <  1:4194489/71‑1 (MQ=255)
                                               aaaCGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGt              <  1:5401449/71‑1 (MQ=255)
                                                accgcgACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTtata             >  1:4471478/3‑71 (MQ=255)
                                                accGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTtata             >  1:3816527/3‑71 (MQ=255)
                                                 ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                     <  1:4133729/45‑1 (MQ=16)
                                                 ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                     <  1:1437401/45‑1 (MQ=16)
                                                 ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                     <  1:1650483/45‑1 (MQ=16)
                                                 ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                     <  1:5020055/45‑1 (MQ=16)
                                                 ccGCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                     <  1:2811956/45‑1 (MQ=16)
                                                  cGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGATTGATTTGTCTTTGTATg           <  1:2826470/71‑1 (MQ=255)
                                                   gCCACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGttt                                     >  1:3198555/1‑44 (MQ=16)
                                                    ccACTTGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGtt                                      >  1:5680876/1‑42 (MQ=16)
                                                      aCTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTg       <  1:298368/71‑1 (MQ=255)
                                                       cTTGCGGTAGCCAGTAACCTTCTTCCCAGAGGCGAAGttt                                     >  1:5490348/1‑40 (MQ=255)
                                                       cTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGttt                                     >  1:5004219/1‑40 (MQ=255)
                                                       cTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGa      <  1:4845245/71‑1 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaa                                  <  1:603560/42‑1 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaaa                                  <  1:4581591/42‑1 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                   <  1:1533551/41‑1 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                   <  1:2062117/41‑1 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTaa                                   <  1:279047/41‑1 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                >  1:2282672/1‑60 (MQ=255)
                                                        ttGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCttt                >  1:1376976/1‑60 (MQ=255)
                                                        ttGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATc                   <  1:4057529/57‑1 (MQ=255)
                                                         tGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCt                  >  1:3091942/1‑57 (MQ=255)
                                                         tGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATc    >  1:1750856/1‑71 (MQ=255)
                                                         tGCGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATc    >  1:3675203/1‑71 (MQ=255)
                                                         tGCGGCAGCCAGTAACTCACTTCCCACAAACGCAGATTGAGATCGAAGGCTTTATCTTtata             >  1:3758542/1‑62 (MQ=255)
                                                          gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                >  1:570752/1‑42 (MQ=255)
                                                          gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                >  1:5088302/1‑42 (MQ=255)
                                                          gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAAt                                >  1:4923259/1‑42 (MQ=255)
                                                          gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                            >  1:1240711/1‑46 (MQ=255)
                                                          gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGaa                            >  1:3399473/1‑46 (MQ=255)
                                                          gCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATcg   >  1:2796996/1‑71 (MQ=255)
                                                           cGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATcg   <  1:2704464/70‑1 (MQ=255)
                                                           cGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATcgc  <  1:4096640/71‑1 (MQ=255)
                                                           cGGCAGCCAGTAACTCTCTTCCCACAAACGCAGTTTGAGATCGAAGGCTTTATCTTTATACGTTTGATcgc  <  1:3651759/71‑1 (MQ=255)
                                                              tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg               <  1:1210079/55‑1 (MQ=255)
                                                              tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg               <  1:2474168/55‑1 (MQ=255)
                                                              tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg               <  1:4445834/55‑1 (MQ=255)
                                                              tAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTg               <  1:1648098/55‑1 (MQ=255)
                                                              |                                                                   
AGATACTCACCGTCAAACAGACCCGTACCAGCAATATCACGTTTACCAAACGCCACTTGCGGTAGCCAGTAACCTTCTTCCCACAGGCGAAGTTTAAAATCGAATGATTTGTCTTTGTATGACTGATCGC  >  Exported/704214‑704343

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