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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,741,977 T→C 36.1% L38L (TTA→TTG)  rseA ← anti‑sigma factor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,741,9770TC36.1% 50.4 / 50.0 83L38L (TTA→TTG) rseAanti‑sigma factor
Reads supporting (aligned to +/- strand):  ref base T (33/20);  new base C (13/17);  total (46/37)
Fisher's exact test for biased strand distribution p-value = 1.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.47e-01

ATCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAAGC  >  minE/1741912‑1742034
                                                                 |                                                         
aTCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTaa                                                         >  1:3309291/1‑68 (MQ=255)
aTCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTaa                                                         >  1:3387930/1‑68 (MQ=255)
 tCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       <  1:220100/69‑1 (MQ=255)
  cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:917301/1‑68 (MQ=255)
  cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:2288032/1‑68 (MQ=255)
  cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:1809235/1‑68 (MQ=255)
  cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:414712/1‑68 (MQ=255)
  cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:3387888/1‑68 (MQ=255)
  cACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGt                                                       >  1:393890/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGGttt                                              >  1:725871/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:937003/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:2670518/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:2911011/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:1706180/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:3367011/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:1491293/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:818934/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:528884/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:11585/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:738566/1‑68 (MQ=255)
           agagATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCtt                                               >  1:1801892/1‑67 (MQ=255)
           agagATATCGAAATGGAGCACCTAGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCttt                                              >  1:2587764/1‑68 (MQ=255)
               atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:417707/1‑69 (MQ=255)
               atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2337008/1‑69 (MQ=255)
               atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2288379/1‑69 (MQ=255)
               atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2168728/1‑69 (MQ=255)
               atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2996478/1‑69 (MQ=255)
               atatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAATCACGGATTAAGTGATAGCTTTCCCAg                                         >  1:2907737/1‑69 (MQ=255)
                tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:3178185/69‑1 (MQ=255)
                tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:376387/69‑1 (MQ=255)
                tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:660467/69‑1 (MQ=255)
                tatCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAgg                                        <  1:1726216/69‑1 (MQ=255)
                  tCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGt                                       >  1:3204744/1‑68 (MQ=255)
                  tCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCAAGGt                                       >  1:1907560/1‑68 (MQ=255)
                    gAAATGGAGCACCTCGGTAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1712667/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3156300/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3258945/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3345234/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:2904983/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:434/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:2782969/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:2639297/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1012565/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1189426/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:132256/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1362083/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1540150/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1803180/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1807187/68‑1 (MQ=255)
                    gAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCAAGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:3237671/68‑1 (MQ=255)
                                 tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTgg                        >  1:891725/1‑68 (MQ=255)
                                 tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTgg                        >  1:841606/1‑68 (MQ=255)
                                 tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTgg                        >  1:3008975/1‑68 (MQ=255)
                                 tCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGT‑ATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:499304/69‑1 (MQ=255)
                                  cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:1020078/69‑1 (MQ=255)
                                  cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:1641977/69‑1 (MQ=255)
                                  cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:1795144/69‑1 (MQ=255)
                                  cGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGt                      <  1:3147320/69‑1 (MQ=255)
                                      aGTATCACCCCGCATTGAGTCACGGATCAAGTGATAGCTTTCCCAGGttt                                     <  1:1795553/50‑1 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTg                                 <  1:2070706/50‑1 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTg                                 <  1:3184830/50‑1 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAgac              >  1:1170337/1‑67 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:1925551/1‑69 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:3122576/1‑69 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:1119267/1‑69 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:2330146/1‑69 (MQ=255)
                                          tCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGcc              >  1:1127040/1‑69 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:2646218/69‑1 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:822207/69‑1 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:2176963/69‑1 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:528252/69‑1 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:2109707/69‑1 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:3055743/69‑1 (MQ=255)
                                            aCCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAg            <  1:3069533/69‑1 (MQ=255)
                                              cccGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGtt          >  1:1441132/1‑69 (MQ=255)
                                                     tGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAag   <  1:2605027/69‑1 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCa             >  1:1285915/1‑58 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:2133250/1‑69 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:125015/1‑69 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:419646/1‑69 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:152891/1‑69 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:1591906/1‑69 (MQ=255)
                                                      gAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAagc  >  1:1634104/1‑69 (MQ=255)
                                                                 |                                                         
ATCACGCGTGAAGAGATATCGAAATGGAGCACCTCGGGAGTATCACCCCGCATTGAGTCACGGATTAAGTGATAGCTTTCCCAGGTTTTCTGCATTTCTGGGTTATGAGCCAGTTCGTTAAGC  >  minE/1741912‑1742034

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