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 1,868,124 T→C 31.9% S259S (TCA→TCG)  ygcU ← predicted FAD containing dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,868,1240TC31.9% 83.8 / 51.3 100S259S (TCA→TCG) ygcUpredicted FAD containing dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (21/47);  new base C (14/18);  total (35/65)
Fisher's exact test for biased strand distribution p-value = 2.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 106 total aligned reads displayed.

TTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGA  >  minE/1868063‑1868191
                                                             |                                                                   
ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATTCAAACGAGCGATTgacggac                                                              >  1:3293625/1‑69 (MQ=255)
ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                                              <  1:2030593/69‑1 (MQ=255)
ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                                              <  1:1791895/69‑1 (MQ=255)
ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                                              >  1:3269741/1‑69 (MQ=255)
ttCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTgacggac                                                              >  1:129776/1‑69 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATAc                                                         <  1:808494/69‑1 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGAt                                                           >  1:1667815/1‑67 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATa                                                          >  1:64794/1‑68 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATa                                                          >  1:3400975/1‑68 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                                         >  1:1724484/1‑69 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                                         >  1:2633777/1‑69 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                                         >  1:3334906/1‑69 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                                         >  1:1435777/1‑69 (MQ=255)
     tCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATAc                                                         >  1:288316/1‑69 (MQ=255)
            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                                                   >  1:849025/1‑68 (MQ=255)
            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                                                   >  1:2181702/1‑68 (MQ=255)
            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                                                   >  1:2660618/1‑68 (MQ=255)
            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                                                   >  1:2039051/1‑68 (MQ=255)
            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                                                   >  1:1755929/1‑68 (MQ=255)
            aaTGGGTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGATACCCTTcc                                                   >  1:1756132/1‑68 (MQ=255)
               gggTGAAGTGTTGTGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:190496/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:940085/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1859393/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1879192/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1933360/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:2496363/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:2720634/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:2766762/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1657497/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:3238198/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1449635/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1440234/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:528403/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:594872/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1163617/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:1141345/56‑1 (MQ=255)
               gggTGAAGTGTTGGGTGCCATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:939438/56‑1 (MQ=255)
                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                                              <  1:3156726/69‑1 (MQ=255)
                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                                              <  1:3248891/69‑1 (MQ=255)
                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                                              <  1:258105/69‑1 (MQ=255)
                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                                              <  1:1041147/69‑1 (MQ=255)
                ggTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCAt                                              <  1:1733276/69‑1 (MQ=255)
                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                                         <  1:1025267/68‑1 (MQ=255)
                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                                         <  1:864324/68‑1 (MQ=255)
                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                                         <  1:1399360/68‑1 (MQ=255)
                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                                         <  1:1666437/68‑1 (MQ=255)
                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                                         <  1:197698/68‑1 (MQ=255)
                      gtgtTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGAttt                                         <  1:2740489/68‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:1612596/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:1268295/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:532619/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:499281/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:1556149/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:1569941/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:2972676/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:1724855/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:2134115/59‑1 (MQ=255)
                           gggTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:2076471/59‑1 (MQ=255)
                                ccATCTTCAGCATCATACAAACGAGCAATCGACGGACGa                                                            <  1:2007406/39‑1 (MQ=25)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACGATGATTTCACGCAGGATGTTGa                          >  1:2097888/1‑68 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:3264592/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:1912391/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:3419303/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:1340929/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:536647/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:1337979/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:1627341/1‑69 (MQ=255)
                                     ttCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGaa                         >  1:2938566/1‑69 (MQ=255)
                                            tCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtt                  >  1:1071885/1‑69 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGTATGTTGAAGCCGGtttt                <  1:1409217/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:3171389/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:903286/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:2508707/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                >  1:3267699/1‑69 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:2873935/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:1422480/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:3335708/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:337983/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:917492/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:923436/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:2785187/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:376705/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:435041/69‑1 (MQ=255)
                                              aTACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:2740488/69‑1 (MQ=255)
                                               tACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:1938993/68‑1 (MQ=255)
                                                aCAAACGAGCGATTGACGGACGATACCCTTCCACCATg                                             <  1:1992067/38‑1 (MQ=255)
                                                 cAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCa              >  1:2378655/1‑68 (MQ=255)
                                                 cAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCa              >  1:207877/1‑68 (MQ=255)
                                                 cAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCAt             >  1:1134834/1‑69 (MQ=255)
                                                 cAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCAt             >  1:2832647/1‑69 (MQ=255)
                                                 cAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCAt             >  1:2799459/1‑69 (MQ=255)
                                                     cGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCt         <  1:1082294/69‑1 (MQ=255)
                                                       aGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGtttt                <  1:2067117/60‑1 (MQ=255)
                                                           aTTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAgg   <  1:1666549/69‑1 (MQ=255)
                                                            ttGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGa  <  1:456159/69‑1 (MQ=255)
                                                            ttGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGa  <  1:3405740/69‑1 (MQ=255)
                                                            ttGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGa  <  1:2175394/69‑1 (MQ=255)
                                                            ttGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGa  <  1:2435504/69‑1 (MQ=255)
                                                            ttGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGa  <  1:246446/69‑1 (MQ=255)
                                                            ttGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGa  <  1:912893/69‑1 (MQ=255)
                                                             |                                                                   
TTCCGTCGGCAAAATGGGTGAAGTGTTGGGTGCCATCTTCAGCGTCATACAAACGAGCGATTGACGGACGATACCCTTCCACCATGATTTCACGCAGGATGTTGAAGCCGGTTTTCATGTCTTCCAGGA  >  minE/1868063‑1868191

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A