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 1,874,126 C→T 29.6% intergenic (+1270/+103) ygcE → / ← ygcF predicted kinase/conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,874,1260CT29.6% 83.9 / 36.8 84intergenic (+1270/+103)ygcE/ygcFpredicted kinase/conserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (22/37);  new base T (16/9);  total (38/46)
Fisher's exact test for biased strand distribution p-value = 3.18e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01

GCAATAATTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCTTTACA  >  minE/1874062‑1874193
                                                                |                                                                   
gCAATAATTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCtt                                                                 <  1:1055268/69‑2 (MQ=255)
gCAATAATTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:1821756/69‑1 (MQ=255)
gCAATAATTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:2975636/69‑1 (MQ=255)
gCAATAATTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:3214720/69‑1 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:2533588/1‑68 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:2308117/1‑68 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:2841105/1‑68 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:3077076/1‑68 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:1078955/1‑68 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:3205161/1‑68 (MQ=255)
     aatTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATg                                                             >  1:2503430/1‑68 (MQ=255)
      atTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:542842/63‑1 (MQ=255)
      atTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:2836542/63‑1 (MQ=255)
      atTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:876200/63‑1 (MQ=255)
      atTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:106764/63‑1 (MQ=255)
      atTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTg                                                                 <  1:2568433/63‑1 (MQ=255)
         ttCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTaa                                                        <  1:2215007/69‑1 (MQ=255)
         ttCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTaa                                                        <  1:2865661/69‑1 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:2119796/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:2723972/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:2292082/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:2032227/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:779209/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:1877395/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:400698/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:3422958/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:1628430/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:3006424/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:930569/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:947608/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:3141654/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:1019957/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGTAGAGAATGATAATGATTAGTCCAGAATg                                                             >  1:101513/1‑62 (MQ=255)
           cACTCCAGCGAAAAATTAACGCCACAGAATTTGT‑‑AGAATGATAATGATTAGTCCAGAATg                                                             >  1:955096/1‑60 (MQ=255)
                   cGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGgaggag                                              <  1:453962/69‑1 (MQ=255)
                       aaaTTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGtttt                                          <  1:1993634/69‑1 (MQ=255)
                       aaaTTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGtttt                                          <  1:2667964/69‑1 (MQ=255)
                       aaaTTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGtttt                                          <  1:1117312/69‑1 (MQ=255)
                       aaaTTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGtttt                                          <  1:2480045/69‑1 (MQ=255)
                        aaTTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGtttt                                          <  1:3095853/68‑1 (MQ=255)
                           tAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCaga                                      <  1:650210/69‑1 (MQ=255)
                           tAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCaga                                      <  1:285367/69‑1 (MQ=255)
                            aaTGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCaga                                      <  1:3371628/68‑1 (MQ=255)
                                  acaGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGACTTTTCAGAGGCGaca                               <  1:3206970/69‑1 (MQ=255)
                                          tGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGtttt                                          <  1:2744961/50‑1 (MQ=255)
                                            tAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAAtata                      <  1:1495003/68‑1 (MQ=255)
                                            tAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAAtata                      <  1:1695758/68‑1 (MQ=255)
                                            tAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAAtata                      <  1:2117153/68‑1 (MQ=255)
                                            tAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAAtata                      <  1:2074045/68‑1 (MQ=255)
                                            tAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAAtata                      <  1:1703746/68‑1 (MQ=255)
                                            tAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAAtata                      <  1:1356914/68‑1 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:1764491/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:1698340/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:2928788/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:292865/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:2881611/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:3120020/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:1076224/1‑69 (MQ=255)
                                                     cTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGa            >  1:2328991/1‑69 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:141238/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:548170/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:1061500/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:3383392/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:1755942/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:835502/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:2688319/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:2318221/69‑1 (MQ=255)
                                                        aTGATTAGTCCAGAATGGGCAAAATGGAGG‑TTTTTCAGAGACGACAAAGAATATAAATGAGTAGAAGTc        <  1:2479705/69‑1 (MQ=255)
                                                          gATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGt         <  1:1259453/67‑1 (MQ=255)
                                                          gATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTc        >  1:99323/1‑68 (MQ=255)
                                                          gATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTc        >  1:3050341/1‑68 (MQ=255)
                                                          gATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTc        >  1:1454054/1‑68 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:2940740/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:2384738/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:2177358/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:2030069/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:139793/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:1307781/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGacaaac                            <  1:1004940/47‑1 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCtt      >  1:2986228/1‑69 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCtt      >  1:2323733/1‑69 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCtt      >  1:896393/1‑69 (MQ=255)
                                                           aTTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCt       >  1:2335982/1‑68 (MQ=255)
                                                             tAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCtt      <  1:1000752/67‑1 (MQ=255)
                                                                cccTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCTTTACa  <  1:2502946/68‑1 (MQ=255)
                                                                cccTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCTTTACa  <  1:796471/68‑1 (MQ=255)
                                                                |                                                                   
GCAATAATTTTCACTCCAGCGAAAAATTAATGCCACAGAATTTGTAGAGAATGCTAATGATTAGCCCTGGATGGGTAAAATGGAGGAGTTTTCAGAGGCGACAAACAATATAAATGAGTAGAAGTCTTTACA  >  minE/1874062‑1874193

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