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 1,923,899 C→T 48.2% T88T (ACC→ACT)  galR → DNA‑binding transcriptional repressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,923,8990CT48.2% 4.7 / 71.9 83T88T (ACC→ACT) galRDNA‑binding transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (39/4);  new base T (17/23);  total (56/27)
Fisher's exact test for biased strand distribution p-value = 3.96e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

GATGTTTCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGCGTCAGGCCATTGAGC  >  minE/1923837‑1923963
                                                              |                                                                
gATGTTTCCGATCCTTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:1744355/68‑1 (MQ=38)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGTCTTATCACACTGGTaa                                                             <  1:751297/68‑1 (MQ=38)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:2401294/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:1784776/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:2083274/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:1722466/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:1842158/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:153768/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:719831/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:2430184/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:581428/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:1372956/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:3375864/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:1149204/68‑1 (MQ=255)
gATGTTTCCGATCCGTTTTTCGGCGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:2410238/68‑1 (MQ=255)
    tttCCGATCCGTTTTTCGGTGCAATGTTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAttttt                                                        <  1:2224382/69‑1 (MQ=255)
    tttCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAttttt                                                        <  1:930217/69‑1 (MQ=255)
    tttCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAttttt                                                        <  1:1800201/69‑1 (MQ=255)
    tttCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAttttt                                                        <  1:2717980/69‑1 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAtttttt                                                       >  1:1867811/1‑68 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAtttttt                                                       >  1:1832280/1‑68 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAAtttttt                                                       >  1:279635/1‑68 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTa                                                      >  1:2600749/1‑69 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTa                                                      >  1:1638176/1‑69 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTa                                                      >  1:2109149/1‑69 (MQ=255)
      tCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTa                                                      >  1:1478977/1‑69 (MQ=255)
                 tttCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTattgatt                                                >  1:3110589/1‑64 (MQ=255)
                 tttCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTattgatt                                                >  1:1783971/1‑64 (MQ=255)
                 tttCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTattgatt                                                >  1:109925/1‑64 (MQ=255)
                 tttCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCaa                                           >  1:2457905/1‑69 (MQ=255)
                 tttCGGTGCAATGGTGAAAGCGCTCGAACATGTGGCTTATCACACCGGTAATTTTTTattgatt                                                >  1:2876607/1‑64 (MQ=255)
                       cgCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTaa                                                             <  1:375715/44‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:1898750/69‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:1844874/69‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:2868194/69‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:1629512/69‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:2541604/69‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:1484921/69‑1 (MQ=255)
                           aTGGTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 <  1:1391967/69‑1 (MQ=255)
                             ggTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACcaca                                >  1:1663365/1‑68 (MQ=255)
                             ggTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACcaca                                >  1:1299768/1‑68 (MQ=255)
                             ggTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACcac                                 >  1:1945393/1‑67 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTattg                                                   >  1:986723/1‑48 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:386239/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:3266328/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:3303961/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:3317889/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:3154881/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:359674/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:2923092/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:946262/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:86295/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:2692153/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:2107395/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:219430/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:67562/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:2204316/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTa                                     >  1:2308707/1‑62 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACTGGTAATTTTTTATTGATTGGCAACGGTTACcaaga                               >  1:129176/1‑65 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACgg                                        >  1:1817081/1‑59 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACgg                                        >  1:2123112/1‑59 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGt                                       >  1:730701/1‑60 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGt                                       >  1:2228189/1‑60 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGt                                       >  1:3051268/1‑60 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGt                                       >  1:1014521/1‑60 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGt                                       >  1:2060705/1‑60 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:102389/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:149695/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:2943153/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:2529183/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:1984573/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:3248807/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:219713/1‑68 (MQ=255)
                              gTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACaa                               >  1:2170538/1‑68 (MQ=255)
                                       gTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACaaa                       >  1:3203032/1‑67 (MQ=255)
                                             cAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGc                 >  1:652621/1‑67 (MQ=255)
                                             cAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGc                 >  1:686057/1‑67 (MQ=255)
                                             cAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGc                 >  1:3214113/1‑67 (MQ=255)
                                             cAGGTCGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGc                 >  1:221685/1‑67 (MQ=255)
                                                          acacCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGCGTCAGGCCATTGAg   >  1:1992241/1‑68 (MQ=255)
                                                          acacCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGCGTCAGGCCATTGAGc  >  1:378974/1‑69 (MQ=255)
                                                          acacCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGCGTCAGGCCATTGAGc  >  1:1562321/1‑69 (MQ=255)
                                                          acacCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGCGTCAGGCCATTGAGc  >  1:3341964/1‑69 (MQ=255)
                                                              |                                                                
GATGTTTCCGATCCGTTTTTCGGTGCAATGGTGAAAGCGGTCGAACAGGTGGCTTATCACACCGGTAATTTTTTATTGATTGGCAACGGTTACCACAACGAACAAAAAGAGCGTCAGGCCATTGAGC  >  minE/1923837‑1923963

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