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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,352,460 T→G intergenic (+103/‑124) yjdJ → / → ghoS GNAT family putative N‑acetyltransferase/antitoxin of GhoTS toxin‑antitoxin pair; endonuclease for ghoT mRNA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,352,4600TG98.1% 184.5 / ‑3.6 54intergenic (+103/‑124)yjdJ/ghoSGNAT family putative N‑acetyltransferase/antitoxin of GhoTS toxin‑antitoxin pair; endonuclease for ghoT mRNA
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (26/26);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

AGTACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGTTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCGTCCCC  >  NC_000913/4352364‑4352553
                                                                                                |                                                                                             
agTACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGgttt                                                                                            <  1:519479/100‑1 (MQ=255)
 gTACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGgtttt                                                                                           <  1:997724/100‑1 (MQ=255)
  tACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGgttttt                                                                                          <  1:893077/100‑1 (MQ=255)
  tACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGgttttt                                                                                          <  2:1172433/100‑1 (MQ=255)
  tACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGgttttt                                                                                          >  2:560710/1‑100 (MQ=255)
   aCAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGGTGCACAAAGAATGGGCAGAGAGCGCGgtttttt                                                                                         >  2:1021350/1‑100 (MQ=255)
    cAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTg                                                                                        <  1:708689/100‑1 (MQ=255)
    cAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTg                                                                                        <  1:673872/100‑1 (MQ=255)
      gagggaCGATATTTTTCATGCGGTCGGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTg                                                                                        <  2:1455213/93‑1 (MQ=255)
         tCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGTGATGCACAACGAATGGGCAGAGAGCGCGGTCGTTTGTc                                                                                      >  2:938232/1‑97 (MQ=255)
          cACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCaa                                                                                  >  1:1279169/1‑100 (MQ=255)
          cACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCa                                                                                   >  1:1000088/1‑99 (MQ=255)
           aCGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCGCAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAg                                                                                 <  2:843116/100‑1 (MQ=255)
            cGATATTTTTTTTTTTTTTTGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCTCaatt                                                                                >  2:418722/1‑98 (MQ=255)
              atatTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCa                                                                              >  1:1459405/1‑100 (MQ=255)
                  ttttCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATcac                                                                          >  2:1433251/1‑98 (MQ=255)
                   tttCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATcccc                                                                         <  2:901469/100‑1 (MQ=255)
                   tttCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATcccc                                                                         <  2:837751/100‑1 (MQ=255)
                    ttCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGATGGGTAGGGGGATGCACAAATAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCt                                                                        <  2:862096/100‑1 (MQ=255)
                      cATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGTGCGCGGTTTTTTGTCCCTAGTCATCCCCtct                                                                      <  1:1064754/100‑3 (MQ=255)
                      cATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCttt                                                                      >  2:324677/1‑100 (MQ=255)
                       aTTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTa                                                                     <  1:694782/100‑1 (MQ=255)
                          ctctcCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTg                                                                  >  2:154725/1‑100 (MQ=255)
                           tctcCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGa                                                                 <  1:256035/100‑1 (MQ=255)
                            ctcCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGan                                                                <  1:352164/100‑2 (MQ=255)
                             tcCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGc                                                               <  1:1274976/100‑1 (MQ=255)
                              ccGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGCGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCa                                                              >  2:1532302/1‑100 (MQ=255)
                                      tgATGCAGGATAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAACAAAAAAAAg                                                      <  2:34197/100‑1 (MQ=255)
                                       gATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGTGGTTTTTTGTCCCAAGTCATCCCCTTTAAAAAGCAAAAAAAAg                                                      <  2:1552536/99‑1 (MQ=255)
                                       gATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGa                                                     >  1:20721/1‑100 (MQ=255)
                                       gATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCAGCCCCTTTACTGAGCaaaaaaaa                                                       >  1:20542/1‑98 (MQ=255)
                                           cAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAatat                                                 >  2:969074/1‑100 (MQ=255)
                                            aGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGTTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATAtc                                                <  1:280399/100‑1 (MQ=255)
                                            aGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATAtc                                                >  1:1346378/1‑100 (MQ=255)
                                                gagCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCt                                            <  1:1336972/100‑1 (MQ=255)
                                                gagCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCt                                            >  2:1576359/1‑100 (MQ=255)
                                                  gCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCtat                                          <  2:732024/100‑1 (MQ=255)
                                                  gCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCtat                                          >  2:819521/1‑100 (MQ=255)
                                                    aTCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTatat                                        >  1:1146154/1‑100 (MQ=255)
                                                      cTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATga                                      >  2:1243780/1‑100 (MQ=255)
                                                         aaGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGaa                                   <  1:324677/100‑1 (MQ=255)
                                                             gTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAatcat                               <  2:421470/100‑1 (MQ=255)
                                                               aGGGGGATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAAtcatca                             <  1:1193143/100‑1 (MQ=255)
                                                                gggggATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCaa                            >  1:166345/1‑100 (MQ=255)
                                                                 ggggATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAAt                           >  1:263186/1‑100 (MQ=255)
                                                                   ggATGCACAAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCg                         <  1:1396585/100‑1 (MQ=255)
                                                                         acaAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTta                   >  1:703584/1‑100 (MQ=255)
                                                                         acaAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTta                   >  1:1274502/1‑100 (MQ=255)
                                                                          caAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTtaa                  >  2:676782/1‑100 (MQ=255)
                                                                          caAAGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTtaa                  <  2:1000081/100‑1 (MQ=255)
                                                                            aaGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTtaata                >  1:1013588/1‑100 (MQ=255)
                                                                            aaGAATGGGCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTtaata                <  2:1274497/100‑1 (MQ=255)
                                                                                  gggCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGtttt          >  2:455465/1‑100 (MQ=255)
                                                                                  gggCAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGtttt          >  1:1044173/1‑100 (MQ=255)
                                                                                     cAGAGAGCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCg       <  1:1021356/100‑1 (MQ=255)
                                                                                     cAGAGAGCGCGCTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATTTGAGAATCATCAATCGGGGTTAATAAGTTTTGCg       >  2:829472/1‑100 (MQ=255)
                                                                                       gagagCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCGTc     <  1:676784/100‑1 (MQ=255)
                                                                                       gagagCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCGTc     >  1:1118250/1‑100 (MQ=255)
                                                                                       gagaaCGCGGTTTTTTGTCCCAAGTCATTCCTTAAAAAAAAAAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCGTc     <  2:1393624/100‑1 (MQ=255)
                                                                                          agCGCGGTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCGTcccc  <  1:774460/100‑1 (MQ=255)
                                                                                                |                                                                                             
AGTACAGAGTCACGATATTTTTCATTCTCTCCGCGATGTGATGCAGGAGAGCATCTGAAGGGTAGGGGGATGCACAAAGAATGGGCAGAGAGCGCGTTTTTTTGTCCCAAGTCATCCCCTTTACTGAGCAAAAAAAAGAATATCTCCTATATGAGAATCATCAATCGGGGTTAATAAGTTTTGCGTCCCC  >  NC_000913/4352364‑4352553

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A