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 F17 I0 R2 278 43.2 2215644 94.6% 2095999 61.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 498,441 C→T 26.6% G24S (GGT→AGT)  galE ← UDP‑galactose‑4‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE498,4410CT26.6% 111.4 / 43.2 64G24S (GGT→AGT) galEUDP‑galactose‑4‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (25/22);  new base T (7/10);  total (32/32)
Fisher's exact test for biased strand distribution p-value = 5.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.53e-01

AACGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCATA  >  minE/498372‑498511
                                                                     |                                                                      
aaCGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGGTGACATCATGACCg                                                                       >  1:499824/1‑71 (MQ=255)
aaCGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGAcc                                                                        <  1:1448583/70‑1 (MQ=255)
 aCGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGt                                                                      <  1:1344557/71‑1 (MQ=255)
    cTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtttt                                                                   >  1:773786/1‑71 (MQ=255)
    cTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGt                                                                      <  1:1491230/68‑1 (MQ=255)
       gATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTg                                                                  >  1:1641992/1‑69 (MQ=255)
       gATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGc                                                                 <  1:2204192/70‑1 (MQ=255)
         tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGt                                                              <  1:614411/71‑1 (MQ=255)
         tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                              <  1:213831/71‑1 (MQ=255)
         tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                              <  1:309262/71‑1 (MQ=255)
          aaCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                              >  1:1800972/1‑70 (MQ=255)
            cAGGAAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAAt                                                           >  1:1623798/1‑71 (MQ=255)
              ggCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTg                                                         >  1:525542/1‑71 (MQ=255)
                  gTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTa                                                             <  1:609357/63‑1 (MQ=255)
                  gTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTa                                                             <  1:2091418/63‑1 (MQ=255)
                   tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGcaca                                                     >  1:65329/1‑70 (MQ=255)
                   tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGcaca                                                     <  1:1640/70‑1 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCatt                                                              >  1:727866/1‑57 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                              >  1:2077341/1‑59 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTaa                                                            >  1:82771/1‑61 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTaa                                                            >  1:707111/1‑61 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                  >  1:2060807/1‑71 (MQ=255)
                     cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                  >  1:1463108/1‑71 (MQ=255)
                          cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTaa                                                            >  1:1806226/1‑56 (MQ=255)
                               aCTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACt                                          <  1:523921/69‑1 (MQ=255)
                               aCTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGGTTTGCAGTAATTGCACACAGGTATGACt                                          <  1:981964/69‑1 (MQ=255)
                               aCTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCATTAATTGcacac                                                    <  1:2024065/59‑1 (MQ=255)
                               aCTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGAc                                           >  1:2167736/1‑68 (MQ=255)
                                   ttACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCa                                      <  1:1875238/69‑1 (MQ=255)
                                      cAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTa                                 <  1:1913766/71‑1 (MQ=255)
                                         agGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAAcc                              >  1:1053035/1‑71 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGt                                                              <  1:856808/36‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGt                                                              <  1:2070805/36‑1 (MQ=255)
                                            ttATCAAGAATGATGACATCATGACTGTTTTGCAGt                                                              <  1:597033/36‑1 (MQ=255)
                                            ttATCAAGAACGATGACATCATGACTGTTTTGCAGt                                                              <  1:1950524/36‑1 (MQ=38)
                                             tATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTa                          >  1:1477749/1‑71 (MQ=255)
                                               tCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                         <  1:166722/70‑1 (MQ=255)
                                                 aaGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTaccac                      >  1:493073/1‑71 (MQ=255)
                                                 aaGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTaccac                      >  1:201570/1‑71 (MQ=255)
                                                   gAATGATGACATCATGACCGTTTTGCAGTAATTGcacac                                                    <  1:715805/39‑1 (MQ=255)
                                                   gAATGATGACATCATGACCGTTTTGCAGTAATTGcacac                                                    <  1:284958/39‑1 (MQ=255)
                                                   gAATGATGACATCATGACCGTTTTGCAGTAATTGcacac                                                    <  1:901216/39‑1 (MQ=255)
                                                    aaTGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTa                                               >  1:931721/1‑43 (MQ=255)
                                                     atgatgACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGt                  <  1:1132651/71‑1 (MQ=255)
                                                      tgatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCg                    >  1:1717560/1‑68 (MQ=255)
                                                      tgatgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCg                    >  1:1680178/1‑68 (MQ=255)
                                                      tgatgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGt                  <  1:1540451/70‑1 (MQ=255)
                                                        atgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               >  1:1092540/1‑71 (MQ=255)
                                                        atgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               >  1:450558/1‑71 (MQ=255)
                                                        atgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               >  1:2210347/1‑71 (MQ=255)
                                                        atgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               <  1:1603530/71‑1 (MQ=255)
                                                          gaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               >  1:1441431/1‑69 (MQ=255)
                                                          gaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               >  1:1632238/1‑69 (MQ=255)
                                                              tcatGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               <  1:1667817/65‑1 (MQ=255)
                                                              tcatGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGaa          <  1:660313/70‑1 (MQ=255)
                                                               catGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc               <  1:1782442/64‑1 (MQ=255)
                                                                atGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc       >  1:997554/1‑71 (MQ=255)
                                                                atGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc       >  1:2073814/1‑71 (MQ=255)
                                                                atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCaa                                     >  1:1273757/1‑41 (MQ=255)
                                                                atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                         >  1:1175156/1‑53 (MQ=255)
                                                                atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc       >  1:1973798/1‑71 (MQ=255)
                                                                 tGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActct      <  1:1623641/71‑1 (MQ=255)
                                                                   aCCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACtctc     <  1:631281/70‑1 (MQ=255)
                                                                   aCCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACtctc     <  1:164175/70‑1 (MQ=255)
                                                                   aCCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCa    <  1:1683650/71‑1 (MQ=255)
                                                                    ccGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCa    >  1:1152461/1‑70 (MQ=255)
                                                                    ccGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCa    <  1:419668/70‑1 (MQ=255)
                                                                     cGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCATa  <  1:318545/71‑1 (MQ=255)
                                                                     |                                                                      
AACGCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCATA  >  minE/498372‑498511

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A