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 1,625,936 C→T 39.3% R11R (CGC→CGT)  tktB → transketolase 2, thiamin‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,625,9360CT39.3% 66.0 / 81.8 122R11R (CGC→CGT) tktBtransketolase 2, thiamin‑binding
Reads supporting (aligned to +/- strand):  ref base C (31/43);  new base T (31/17);  total (62/60)
Fisher's exact test for biased strand distribution p-value = 1.67e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

Only 100 of 122 total aligned reads displayed.

CCAAACTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATG  >  minE/1625874‑1625999
                                                              |                                                               
ccAAACTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTc                                                           <  1:1393633/69‑1 (MQ=255)
  aaaCTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCat                                                         <  1:2829974/69‑2 (MQ=255)
  aaaCTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:2013469/69‑1 (MQ=255)
   aaCTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:3018335/68‑1 (MQ=255)
   aaCTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:51050/68‑1 (MQ=255)
      tataAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:2183184/69‑1 (MQ=255)
      tataAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:2064343/69‑1 (MQ=255)
      tataAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:1324657/69‑1 (MQ=255)
      tataAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:1697057/69‑1 (MQ=255)
                     gAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACaaaaa                                      >  1:2215444/1‑69 (MQ=255)
                     gAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACaaaaa                                      >  1:368771/1‑69 (MQ=255)
                     gAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACaaaaa                                      >  1:1339366/1‑69 (MQ=255)
                     gAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACaaaaa                                      >  1:3284820/1‑69 (MQ=255)
                     gAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACaaaaa                                      >  1:68100/1‑69 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTAt                                                      >  1:715407/1‑48 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:3020855/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     >  1:3147803/1‑49 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:3234606/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:119388/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:30349/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:2577549/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:3369913/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:1723624/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:1475004/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:2712514/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:1243200/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:2637800/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:130713/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:1358656/49‑1 (MQ=255)
                          ttATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATg                                                     <  1:906853/49‑1 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:1215732/40‑1 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:3263383/40‑1 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:2532102/40‑1 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAg                                                         <  1:258615/40‑1 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAActct                             >  1:488779/1‑68 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAActct                             >  1:3012838/1‑68 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:2417850/1‑69 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:2273669/1‑69 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:1943670/1‑69 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:2140491/1‑69 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:373367/1‑69 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:2805877/1‑69 (MQ=255)
                               tGTCCCGAAAAGACCTTGCCAATGAGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTg                            >  1:1023709/1‑69 (MQ=255)
                                 tCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGt                          >  1:2040637/1‑69 (MQ=255)
                                 tCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGt                          >  1:2397519/1‑69 (MQ=255)
                                 tCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGt                          >  1:681678/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:2479909/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:2726542/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:2061418/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:296884/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:3048464/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:3278930/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:1277167/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:1229248/1‑69 (MQ=255)
                                   ccGAAAAGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCa                        >  1:1104030/1‑69 (MQ=255)
                                     gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                       <  1:1734604/68‑1 (MQ=255)
                                     gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                       <  1:1459215/68‑1 (MQ=255)
                                     gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                       <  1:778749/68‑1 (MQ=255)
                                     gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                       <  1:2861694/68‑1 (MQ=255)
                                     gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                       <  1:1093132/68‑1 (MQ=255)
                                     gAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCAt                       <  1:954214/68‑1 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGTATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:648555/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:3296673/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:2464373/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:539836/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:734957/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:2634592/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:1087918/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:1415511/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:1416057/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:1919644/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:1982947/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:2412863/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:2504303/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:2621372/1‑69 (MQ=255)
                                      aaaaGACCTTGCCAATGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATcc                     >  1:2550767/1‑69 (MQ=255)
                                        aaGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATccc                    >  1:228045/1‑68 (MQ=255)
                                        aaGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCg                   >  1:2820480/1‑69 (MQ=255)
                                               tGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGcc            <  1:415433/69‑1 (MQ=255)
                                               tGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGcc            <  1:1954964/69‑1 (MQ=255)
                                               tGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGcc            <  1:2089424/69‑1 (MQ=255)
                                                 ccAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGa          >  1:2024366/1‑69 (MQ=255)
                                                 ccAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGa          >  1:2519105/1‑69 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:2192206/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:3056410/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:942172/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:913926/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:111743/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:3159474/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:1768007/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:1835294/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:2410662/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:226248/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:2454749/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:394137/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:2239912/63‑1 (MQ=255)
                                                     tGCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:2221211/63‑1 (MQ=255)
                                                      gCGATTCGTGCACTCAGTATGGATGCGGTACAAAAAGCCAATTCTGGTCATCCCGGCGCGcc            <  1:1660726/62‑1 (MQ=255)
                                                         aTTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATg  <  1:1852300/69‑1 (MQ=255)
                                                         aTTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATg  <  1:2592237/69‑1 (MQ=255)
                                                              |                                                               
CCAAACTATAAACCAGCCACGGAGTGTTATATGTCCCGAAAAGACCTTGCCAATGCGATTCGCGCACTCAGTATGGATGCGGTACAAAAAGCCAACTCTGGTCATCCCGGCGCGCCGATGGGCATG  >  minE/1625874‑1625999

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A